Merge branch 'lammps:develop' into spica-kk

.github/CODEOWNERS

@@ -59,7 +59,8 @@ src/VTK/*             @rbberger
 
 # individual files in packages
 src/GPU/pair_vashishta_gpu.*        @andeplane
-src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
+src/KOKKOS/pair_vashishta_kokkos.*  @andeplane @stanmoore1
+src/KOSSOS/pair_pod_kokkos.*        @exapde @stanmoore1
 src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
 src/MANYBODY/pair_nb3b_screened.*   @flodesani

.gitignore

@@ -43,12 +43,12 @@ Thumbs.db
 
 #cmake
 /build*
-/CMakeCache.txt
+CMakeCache.txt
-/CMakeFiles/
+CMakeFiles
-/Testing
 /Makefile
-/Testing
+Testing
-/cmake_install.cmake
+Temporary
+cmake_install.cmake
 /lmp
 out/Debug
 out/RelWithDebInfo
@@ -60,3 +60,4 @@ src/Makefile.package.settings-e
 /cmake/build/x64-Debug-Clang
 /install/x64-GUI-MSVC
 /install
+.Rhistory

cmake/CMakeLists.txt

@@ -23,6 +23,7 @@ project(lammps CXX)
 set(SOVERSION 0)
 get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
 
+include(GNUInstallDirs)
 get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
 # collect all executables and shared libs in the top level build folder
@@ -163,6 +164,22 @@ if(MSVC)
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
+# warn about potentially problematic GCC compiler versions
+if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+  if (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
+      message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
+        "with C++17 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 9.x or later")
+    endif()
+  endif()
+  if (CMAKE_CXX_STANDARD GREATER_EQUAL 11)
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
+      message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
+        "with C++11 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 5.x or later")
+    endif()
+  endif()
+endif()
+
 # export all symbols when building a .dll file on windows
 if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
   set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
@@ -197,18 +214,17 @@ set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
 option(BUILD_SHARED_LIBS "Build shared library" OFF)
 option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
-option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" 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,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")
+  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()
 
-include(GNUInstallDirs)
+
 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})
@@ -282,10 +298,10 @@ set(STANDARD_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-PACE
+  ML-POD
   ML-QUIP
   ML-RANN
   ML-SNAP
-  ML-POD
   ML-UF3
   MOFFF
   MOLECULE
@@ -305,6 +321,7 @@ set(STANDARD_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK
@@ -409,6 +426,7 @@ pkg_depends(CG-DNA ASPHERE)
 pkg_depends(ELECTRODE KSPACE)
 pkg_depends(EXTRA-MOLECULE MOLECULE)
 pkg_depends(MESONT MOLECULE)
+pkg_depends(RHEO BPM)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -549,7 +567,7 @@ else()
 endif()
 
 foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
-        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON)
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON RHEO)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -939,6 +957,7 @@ message(STATUS "<<< Compilers and Flags: >>>
 -- C++ Compiler:     ${CMAKE_CXX_COMPILER}
       Type:          ${CMAKE_CXX_COMPILER_ID}
       Version:       ${CMAKE_CXX_COMPILER_VERSION}
+      C++ Standard:  ${CMAKE_CXX_STANDARD}
       C++ Flags:    ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
       Defines:       ${DEFINES}")
 get_target_property(OPTIONS lammps COMPILE_OPTIONS)
@@ -1045,9 +1064,6 @@ endif()
 if(BUILD_TOOLS)
   message(STATUS "<<< Building Tools >>>")
 endif()
-if(BUILD_LAMMPS_SHELL)
-  message(STATUS "<<< Building LAMMPS Shell >>>")
-endif()
 if(BUILD_LAMMPS_GUI)
   message(STATUS "<<< Building LAMMPS GUI >>>")
   if(LAMMPS_GUI_USE_PLUGIN)

cmake/Modules/Packages/ML-QUIP.cmake

@@ -27,7 +27,7 @@ if(DOWNLOAD_QUIP)
   else()
     message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
   endif()
-  set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
+  set(temp "${temp}CFLAGS += -fPIC -Wno-return-mismatch \nCPLUSPLUSFLAGS += -fPIC -Wno-return-mismatch\nAR_ADD=src\n")
   set(temp "${temp}MATH_LINKOPTS=")
   foreach(flag ${BLAS_LIBRARIES})
     set(temp "${temp} ${flag}")

cmake/Modules/Packages/RHEO.cmake

@@ -0,0 +1,2 @@
+find_package(GSL 2.7 REQUIRED)
+target_link_libraries(lammps PRIVATE GSL::gsl)

cmake/Modules/Testing.cmake

@@ -102,9 +102,9 @@ endif()
 #######################################
 # select code sanitizer options
 #######################################
-set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
+set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, hwaddress, leak, thread, undefined)")
 mark_as_advanced(ENABLE_SANITIZER)
-set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
+set(ENABLE_SANITIZER_VALUES none address hwaddress leak thread undefined)
 set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
 validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
 string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)

cmake/Modules/Tools.cmake

@@ -37,37 +37,6 @@ if(BUILD_TOOLS)
   add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
 endif()
 
-find_package(PkgConfig QUIET)
-if(BUILD_LAMMPS_SHELL)
-  if(NOT PkgConfig_FOUND)
-    message(FATAL_ERROR "Must have pkg-config installed for building LAMMPS shell")
-  endif()
-  find_package(PkgConfig REQUIRED)
-  pkg_check_modules(READLINE IMPORTED_TARGET REQUIRED readline)
-
-  # include resource compiler to embed icons into the executable on Windows
-  if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
-    enable_language(RC)
-    set(ICON_RC_FILE ${LAMMPS_TOOLS_DIR}/lammps-shell/lmpicons.rc)
-  endif()
-
-  add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp ${ICON_RC_FILE})
-  target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
-  target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
-
-  # workaround for broken readline pkg-config file on FreeBSD
-  if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD")
-    target_include_directories(lammps-shell PRIVATE /usr/local/include)
-  endif()
-  if(CMAKE_SYSTEM_NAME STREQUAL "LinuxMUSL")
-    pkg_check_modules(TERMCAP IMPORTED_TARGET REQUIRED termcap)
-    target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::TERMCAP)
-  endif()
-  install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
-  install(DIRECTORY ${LAMMPS_TOOLS_DIR}/lammps-shell/icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
-  install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
-endif()
-
 if(BUILD_LAMMPS_GUI)
   get_filename_component(LAMMPS_GUI_DIR ${LAMMPS_SOURCE_DIR}/../tools/lammps-gui ABSOLUTE)
   get_filename_component(LAMMPS_GUI_BIN ${CMAKE_BINARY_DIR}/lammps-gui-build ABSOLUTE)

cmake/presets/all_off.cmake

@@ -26,8 +26,8 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
   EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
@@ -82,6 +82,7 @@ set(ALL_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK

cmake/presets/all_on.cmake

@@ -28,8 +28,8 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
   EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
@@ -84,6 +84,7 @@ set(ALL_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK

cmake/presets/mingw-cross.cmake

@@ -22,8 +22,8 @@ set(WIN_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
   EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
@@ -33,7 +33,6 @@ set(WIN_PACKAGES
   FEP
   GPU
   GRANULAR
-  INTEL
   INTERLAYER
   KSPACE
   LEPTON

cmake/presets/windows.cmake

@@ -52,8 +52,8 @@ set(WIN_PACKAGES
   ORIENT
   PERI
   PHONON
-  POEMS
   PLUGIN
+  POEMS
   PTM
   QEQ
   QTB

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "17 April 2024" "2024-04-17"
+.TH LAMMPS "1" "27 June 2024" "2024-06-27"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 17 April 2024
+\- Molecular Dynamics Simulator.  Version 27 June 2024
 
 .SH SYNOPSIS
 .B lmp

doc/src/Build_basics.rst

@@ -489,8 +489,7 @@ using CMake or Make.
       .. code-block:: bash
 
          -D BUILD_TOOLS=value         # yes or no (default). Build binary2txt, chain.x, micelle2d.x, msi2lmp, phana, stl_bin2txt
-         -D BUILD_LAMMPS_SHELL=value  # yes or no (default). Build lammps-shell
+         -D BUILD_LAMMPS_GUI=value    # yes or no (default). Build LAMMPS-GUI
-         -D BUILD_LAMMPS_GUI=value    # yes or no (default). Build lammps-gui
 
       The generated binaries will also become part of the LAMMPS installation
       (see below).
@@ -505,8 +504,9 @@ using CMake or Make.
          make chain            # build only chain tool
          make micelle2d        # build only micelle2d tool
 
-         cd lammps/tools/lammps-shell
+      .. note::
-         make                  # build LAMMPS shell
+
+         Building the LAMMPS-GUI *requires* building LAMMPS with CMake.
 
 ----------
 

doc/src/Build_development.rst

@@ -88,8 +88,8 @@ on recording all commands required to do the compilation.
 
 .. _sanitizer:
 
-Address, Undefined Behavior, and Thread Sanitizer Support (CMake only)
+Address, Leak, Undefined Behavior, and Thread Sanitizer Support (CMake only)
-----------------------------------------------------------------------
+----------------------------------------------------------------------------
 
 Compilers such as GCC and Clang support generating instrumented binaries
 which use different sanitizer libraries to detect problems in the code
@@ -110,6 +110,7 @@ compilation and linking stages.  This is done through setting the
 
    -D ENABLE_SANITIZER=none       # no sanitizer active (default)
    -D ENABLE_SANITIZER=address    # enable address sanitizer / memory leak checker
+   -D ENABLE_SANITIZER=hwaddress  # enable hardware assisted address sanitizer / memory leak checker
    -D ENABLE_SANITIZER=leak       # enable memory leak checker (only)
    -D ENABLE_SANITIZER=undefined  # enable undefined behavior sanitizer
    -D ENABLE_SANITIZER=thread     # enable thread sanitizer

doc/src/Build_extras.rst

@@ -59,6 +59,7 @@ This is the list of packages that may require additional steps.
    * :ref:`POEMS <poems>`
    * :ref:`PYTHON <python>`
    * :ref:`QMMM <qmmm>`
+   * :ref:`RHEO <rheo>`
    * :ref:`SCAFACOS <scafacos>`
    * :ref:`VORONOI <voronoi>`
    * :ref:`VTK <vtk>`
@@ -1566,10 +1567,11 @@ LAMMPS build.
    .. tab:: CMake build
 
       When the ``-D PKG_PLUMED=yes`` flag is included in the cmake
-      command you must ensure that GSL is installed in locations that
+      command you must ensure that `the GNU Scientific Library (GSL)
-      are specified in your environment.  There are then two additional
+      <https://www.gnu.org/software/gsl/>` is installed in locations
-      variables that control the manner in which PLUMED is obtained and
+      that are accessible in your environment.  There are then two
-      linked into LAMMPS.
+      additional variables that control the manner in which PLUMED is
+      obtained and linked into LAMMPS.
 
       .. code-block:: bash
 
@@ -2040,6 +2042,36 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 
 ----------
 
+.. _rheo:
+
+RHEO package
+------------
+
+To build with this package you must have the `GNU Scientific Library
+(GSL) <https://www.gnu.org/software/gsl/>` installed in locations that
+are accessible in your environment.  The GSL library should be at least
+version 2.7.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      If CMake cannot find the GSL library or include files, you can set:
+
+      .. code-block:: bash
+
+         -D GSL_ROOT_DIR=path    # path to root of GSL installation
+
+   .. tab:: Traditional make
+
+      LAMMPS will try to auto-detect the GSL compiler and linker flags
+      from the corresponding ``pkg-config`` file (``gsl.pc``), otherwise
+      you can edit the file ``lib/rheo/Makefile.lammps``
+      to specify the paths and library names where indicated by comments.
+      This must be done **before** the package is installed.
+
+----------
+
 .. _scafacos:
 
 SCAFACOS package

doc/src/Build_link.rst

@@ -45,8 +45,8 @@ executable code from the library is copied into the calling executable.
 
       .. code-block:: bash
 
-         mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+         mpicc -c -O $(pkg-config --cflags liblammps) caller.c
-         mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
+         mpicxx -o caller caller.o -$(pkg-config --libs liblammps)
 
    .. tab:: Traditional make
 
@@ -155,8 +155,8 @@ POEMS package installed becomes:
 
       .. code-block:: bash
 
-         mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+         mpicc -c -O $(pkg-config --cflags liblammps) caller.c
-         mpicxx -o caller caller.o -$(pkgconf --libs)
+         mpicxx -o caller caller.o -$(pkg-config --libs liblammps)
 
    .. tab:: Traditional make
 

doc/src/Build_package.rst

@@ -62,6 +62,7 @@ packages:
    * :ref:`POEMS <poems>`
    * :ref:`PYTHON <python>`
    * :ref:`QMMM <qmmm>`
+   * :ref:`RHEO <rheo>`
    * :ref:`SCAFACOS <scafacos>`
    * :ref:`VORONOI <voronoi>`
    * :ref:`VTK <vtk>`

doc/src/Commands_bond.rst

@@ -54,6 +54,7 @@ OPT.
    * :doc:`oxdna2/fene <bond_oxdna>`
    * :doc:`oxrna2/fene <bond_oxdna>`
    * :doc:`quartic (o) <bond_quartic>`
+   * :doc:`rheo/shell <bond_rheo_shell>`
    * :doc:`special <bond_special>`
    * :doc:`table (o) <bond_table>`
 

doc/src/Commands_compute.rst

@@ -108,6 +108,10 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`pe/mol/tally <compute_tally>`
    * :doc:`pe/tally <compute_tally>`
    * :doc:`plasticity/atom <compute_plasticity_atom>`
+   * :doc:`pod/atom <compute_pod_atom>`
+   * :doc:`podd/atom <compute_pod_atom>`
+   * :doc:`pod/local <compute_pod_atom>`
+   * :doc:`pod/global <compute_pod_atom>`
    * :doc:`pressure <compute_pressure>`
    * :doc:`pressure/alchemy <compute_pressure_alchemy>`
    * :doc:`pressure/uef <compute_pressure_uef>`
@@ -122,6 +126,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`reduce <compute_reduce>`
    * :doc:`reduce/chunk <compute_reduce_chunk>`
    * :doc:`reduce/region <compute_reduce>`
+   * :doc:`rheo/property/atom <compute_rheo_property_atom>`
    * :doc:`rigid/local <compute_rigid_local>`
    * :doc:`saed <compute_saed>`
    * :doc:`slcsa/atom <compute_slcsa_atom>`

doc/src/Commands_fix.rst

@@ -28,6 +28,7 @@ OPT.
    * :doc:`adapt <fix_adapt>`
    * :doc:`adapt/fep <fix_adapt_fep>`
    * :doc:`addforce <fix_addforce>`
+   * :doc:`add/heat <fix_add_heat>`
    * :doc:`addtorque <fix_addtorque>`
    * :doc:`alchemy <fix_alchemy>`
    * :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
@@ -204,6 +205,11 @@ OPT.
    * :doc:`reaxff/species (k) <fix_reaxff_species>`
    * :doc:`recenter <fix_recenter>`
    * :doc:`restrain <fix_restrain>`
+   * :doc:`rheo <fix_rheo>`
+   * :doc:`rheo/oxidation <fix_rheo_oxidation>`
+   * :doc:`rheo/pressure <fix_rheo_pressure>`
+   * :doc:`rheo/thermal <fix_rheo_thermal>`
+   * :doc:`rheo/viscosity <fix_rheo_viscosity>`
    * :doc:`rhok <fix_rhok>`
    * :doc:`rigid (o) <fix_rigid>`
    * :doc:`rigid/meso <fix_rigid_meso>`

doc/src/Commands_pair.rst

@@ -35,6 +35,10 @@ OPT.
    *
    *
    *
+   *
+   *
+   *
+   *
    * :doc:`adp (ko) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
    * :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
@@ -247,7 +251,7 @@ OPT.
    * :doc:`pace (k) <pair_pace>`
    * :doc:`pace/extrapolation (k) <pair_pace>`
    * :doc:`pedone (o) <pair_pedone>`
-   * :doc:`pod <pair_pod>`
+   * :doc:`pod (k) <pair_pod>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`
@@ -260,6 +264,8 @@ OPT.
    * :doc:`rebo (io) <pair_airebo>`
    * :doc:`rebomos (o) <pair_rebomos>`
    * :doc:`resquared (go) <pair_resquared>`
+   * :doc:`rheo <pair_rheo>`
+   * :doc:`rheo/solid <pair_rheo_solid>`
    * :doc:`saip/metal (t) <pair_saip_metal>`
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
    * :doc:`smatb <pair_smatb>`

doc/src/Commands_removed.rst

@@ -8,6 +8,18 @@ stop LAMMPS and print a suitable error message in most cases, when a
 style/command is used that has been removed or will replace the command
 with the direct alternative (if available) and print a warning.
 
+restart2data tool
+-----------------
+
+.. versionchanged:: 23Nov2013
+
+The functionality of the restart2data tool has been folded into the
+LAMMPS executable directly instead of having a separate tool.  A
+combination of the commands :doc:`read_restart <read_restart>` and
+:doc:`write_data <write_data>` can be used to the same effect.  For
+added convenience this conversion can also be triggered by
+:doc:`command line flags <Run_options>`
+
 Fix ave/spatial and fix ave/spatial/sphere
 ------------------------------------------
 
@@ -151,17 +163,16 @@ and allow running LAMMPS with GPU acceleration.
 i-PI tool
 ---------
 
-.. versionchanged:: TBD
+.. versionchanged:: 27Jun2024
 
 The i-PI tool has been removed from the LAMMPS distribution.  Instead,
-instructions to install i-PI from PyPi via pip are provided.
+instructions to install i-PI from PyPI via pip are provided.
 
-restart2data tool
+LAMMPS shell
------------------
+------------
+
+.. versionchanged:: TBD
+
+The LAMMPS shell has been removed from the LAMMPS distribution. Users
+are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
 
-The functionality of the restart2data tool has been folded into the
-LAMMPS executable directly instead of having a separate tool.  A
-combination of the commands :doc:`read_restart <read_restart>` and
-:doc:`write_data <write_data>` can be used to the same effect.  For
-added convenience this conversion can also be triggered by
-:doc:`command line flags <Run_options>`

doc/src/Developer_utils.rst

@@ -211,6 +211,9 @@ Argument processing
 .. doxygenfunction:: bounds
    :project: progguide
 
+.. doxygenfunction:: bounds_typelabel
+   :project: progguide
+
 .. doxygenfunction:: expand_args
    :project: progguide
 

doc/src/Developer_write_pair.rst

@@ -50,6 +50,30 @@ We are looking at the following cases:
 - `Case 3: a potential requiring communication`_
 - `Case 4: potentials without a compute() function`_
 
+Package and build system considerations
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In general, new pair styles should be added to the :ref:`EXTRA-PAIR
+package <PKG-EXTRA-PAIR>` unless they are an accelerated pair style and
+then they should be added to the corresponding accelerator package
+(:ref:`GPU <PKG-GPU>`, :ref:`INTEL <PKG-INTEL>`, :ref:`KOKKOS
+<PKG-KOKKOS>`, :ref:`OPENMP <PKG-OPENMP>`, :ref:`OPT <PKG-OPT>`).  If
+you feel that your contribution should be added to a different package,
+please consult with the LAMMPS developers first.
+
+The contributed code needs to support the :doc:`traditional GNU make
+build process <Build_make>` **and** the :doc:`CMake build process
+<Build_cmake>`.  For the GNU make process and if the package has an
+``Install.sh`` file, most likely that file needs to be updated to
+correctly copy the sources when installing the package and properly
+delete them when uninstalling.  This is particularly important when
+added a new pair style that is a derived class from an existing pair
+style in a package, so that its installation depends on the the
+installation status of the package of the derived class.  For the CMake
+process, it is sometimes necessary to make changes to the package
+specific CMake scripting in ``cmake/Modules/Packages``.
+
+
 ----
 
 Case 1: a pairwise additive model

doc/src/Examples.rst

@@ -134,6 +134,8 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | rerun       | use of rerun and read_dump commands                              |
 +-------------+------------------------------------------------------------------+
+| rheo        | RHEO simulations of fluid flows and phase transitions            |
++-------------+------------------------------------------------------------------+
 | rigid       | rigid bodies modeled as independent or coupled                   |
 +-------------+------------------------------------------------------------------+
 | shear       | sideways shear applied to 2d solid, with and without a void      |

doc/src/Fortran.rst

@@ -2327,7 +2327,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    retrieved via :f:func:`get_last_error_message`.  This allows to
    restart a calculation or delete and recreate the LAMMPS instance when
    a C++ exception occurs.  One application of using exceptions this way
-   is the :ref:`lammps_shell`.
+   is the :ref:`lammps_gui`.
 
    :to: :cpp:func:`lammps_config_has_exceptions`
    :r has_exceptions:

doc/src/Howto.rst

@@ -89,6 +89,7 @@ Packages howto
    Howto_drude2
    Howto_peri
    Howto_manifold
+   Howto_rheo
    Howto_spins
 
 Tutorials howto

doc/src/Howto_bioFF.rst

@@ -1,6 +1,10 @@
 CHARMM, AMBER, COMPASS, and DREIDING force fields
 =================================================
 
+A compact summary of the concepts, definitions, and properties of
+force fields with explicit bonded interactions (like the ones discussed
+in this HowTo) is given in :ref:`(Gissinger) <Typelabel2>`.
+
 A force field has 2 parts: the formulas that define it and the
 coefficients used for a particular system.  Here we only discuss
 formulas implemented in LAMMPS that correspond to formulas commonly used
@@ -11,12 +15,42 @@ commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
 <bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc page for
 additional tools that can use CHARMM, AMBER, or Materials Studio
 generated files to assign force field coefficients and convert their
-output into LAMMPS input.
+output into LAMMPS input. LAMMPS input scripts can also be generated by
+`charmm-gui.org <https://charmm-gui.org/>`_.
 
-See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM
+CHARMM and AMBER
-force field.  See :ref:`(Cornell) <howto-Cornell>` for a description of
+----------------
-the AMBER force field.  See :ref:`(Sun) <howto-Sun>` for a description
+
-of the COMPASS force field.
+The `CHARMM force field
+<https://mackerell.umaryland.edu/charmm_ff.shtml>`_ :ref:`(MacKerell)
+<howto-MacKerell>` and `AMBER force field
+<https://ambermd.org/AmberModels.php>`_ :ref:`(Cornell) <howto-Cornell>`
+have potential energy function of the form
+
+.. math::
+
+  V & = \sum_{bonds} E_b + \sum_{angles} \!E_a + \!\overbrace{\sum_{dihedral} \!\!E_d}^{\substack{
+         \text{charmm} \\
+        \text{charmmfsw}
+      }} +\!\!\! \sum_{impropers} \!\!\!E_i \\[.6em]
+      & \quad + \!\!\!\!\!\!\!\!\!\!\underbrace{~\sum_{pairs} \left(E_{LJ}+E_{coul}\right)}_{\substack{
+         \text{lj/charmm/coul/charmm} \\
+        \text{lj/charmm/coul/charmm/implicit} \\
+        \text{lj/charmm/coul/long} \\
+        \text{lj/charmm/coul/msm} \\
+         \text{lj/charmmfsw/coul/charmmfsh} \\
+        \text{lj/charmmfsw/coul/long}
+      }} \!\!\!\!\!\!\!\!+ \!\!\sum_{special}\! E_s + \!\!\!\!\sum_{residues} \!\!\!{\scriptstyle\mathrm{CMAP}(\phi,\psi)}
+
+
+The terms are computed by bond styles (relationship between 2 atoms),
+angle styles (between 3 atoms) , dihedral/improper styles (between 4
+atoms), pair styles (non-covalently bonded pair interactions) and
+special bonds. The CMAP term (see :doc:`fix cmap <fix_cmap>` command for
+details) corrects for pairs of dihedral angles ("Correction MAP") to
+significantly improve the structural and dynamic properties of proteins
+in crystalline and solution environments :ref:`(Brooks)
+<howto-Brooks>`. The AMBER force field does not include the CMAP term.
 
 The interaction styles listed below compute force field formulas that
 are consistent with common options in CHARMM or AMBER.  See each
@@ -31,10 +65,81 @@ command's documentation for the formula it computes.
 * :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm
 * :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm/implicit
 * :doc:`pair_style <pair_charmm>` lj/charmm/coul/long
-
 * :doc:`special_bonds <special_bonds>` charmm
 * :doc:`special_bonds <special_bonds>` amber
 
+The pair styles compute Lennard Jones (LJ) and Coulombic interactions
+with additional switching or shifting functions that ramp the energy
+and/or force smoothly to zero between an inner :math:`(a)` and outer
+:math:`(b)` cutoff. The older styles with *charmm* (not *charmmfsw* or
+*charmmfsh*\ ) in their name compute the LJ and Coulombic interactions
+with an energy switching function (esw) S(r) which ramps the energy
+smoothly to zero between the inner and outer cutoff. This can cause
+irregularities in pairwise forces (due to the discontinuous second
+derivative of energy at the boundaries of the switching region), which
+in some cases can result in complications in energy minimization and
+detectable artifacts in MD simulations.
+
+.. grid:: 1 1 2 2
+
+   .. grid-item::
+
+      .. math::
+
+         LJ(r) &= 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
+                  \left(\frac{\sigma}{r}\right)^6 \right]\\[.6em]
+         C(r) &= \frac{C q_i q_j}{ \epsilon r}\\[.6em]
+         S(r) &=  \frac{ \left(b^2 - r^2\right)^2 \left(b^2 + 2r^2 - 3{a^2}\right)}
+                 { \left(b^2 - a^2\right)^3 }\\[.6em]
+         E_{LJ}(r) &=  \begin{cases}
+           LJ(r), & r \leq a \\
+           LJ(r) S(r), & a < r \leq b \\
+           0, &r > b
+         \end{cases} \\[.6em]
+         E_{coul}(r) &=  \begin{cases}
+           C(r), & r \leq a \\
+           C(r) S(r), & a < r \leq b \\
+           0, & r > b
+         \end{cases}
+
+   .. grid-item::
+
+      .. image:: img/howto_charmm_ELJ.png
+         :align: center
+
+The newer styles with *charmmfsw* or *charmmfsh* in their name replace
+energy switching with force switching (fsw) for LJ interactions and
+force shifting (fsh) functions for Coulombic interactions
+:ref:`(Steinbach) <howto-Steinbach>`
+
+.. grid:: 1 1 2 2
+
+   .. grid-item::
+
+      .. math::
+
+           E_{LJ}(r) = & \begin{cases}
+       4  \epsilon \sigma^6  \left(\frac{\displaystyle\sigma
+         ^6-r^6}{\displaystyle r^{12}}-\frac{\displaystyle\sigma ^6}{\displaystyle a^6
+         b^6}+\frac{\displaystyle 1}{\displaystyle a^3 b^3}\right) & r\leq a \\
+       \frac{\displaystyle 4 \epsilon \sigma^6   \left(\sigma ^6
+         \left(b^6-r^6\right)^2-b^3 r^6 \left(a^3+b^3\right)
+         \left(b^3-r^3\right)^2\right)}{\displaystyle b^6 r^{12}
+         \left(b^6-a^6\right)} & a<r \leq b\\
+         0, & r>b
+        \end{cases}\\[.6em]
+         E_{coul}(r) & =  \begin{cases}
+              C(r) \frac{\displaystyle (b-r)^2}{\displaystyle r b^2}, &  r \leq b \\
+              0, & r > b
+            \end{cases}
+
+   .. grid-item::
+      .. image:: img/howto_charmmfsw_ELJ.png
+         :align: center
+
+These styles are used by LAMMPS input scripts generated by
+https://charmm-gui.org/ :ref:`(Brooks) <howto-Brooks>`.
+
 .. note::
 
    For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in
@@ -43,17 +148,33 @@ command's documentation for the formula it computes.
    <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
    pages.
 
+.. note::
+
+  The TIP3P water model is strongly recommended for use with the CHARMM
+  force field. In fact, `"using the SPC model with CHARMM parameters is
+  a bad idea"
+  <https://matsci.org/t/using-spc-water-with-charmm-ff/24715>`_ and `"to
+  enable TIP4P style water in CHARMM, you would have to write a new pair
+  style"
+  <https://matsci.org/t/hybrid-pair-styles-for-charmm-and-tip4p-ew/32609>`_
+  . LAMMPS input scripts generated by Solution Builder on https://charmm-gui.org
+  use TIP3P molecules for solvation.  Any other water model can and
+  probably will lead to false conclusions.
+
+COMPASS
+-------
+
 COMPASS is a general force field for atomistic simulation of common
 organic molecules, inorganic small molecules, and polymers which was
-developed using ab initio and empirical parameterization techniques.
+developed using ab initio and empirical parameterization techniques
-See the :doc:`Tools <Tools>` page for the msi2lmp tool for creating
+:ref:`(Sun) <howto-Sun>`.  See the :doc:`Tools <Tools>` page for the
-LAMMPS template input and data files from BIOVIA's Materials Studio
+msi2lmp tool for creating LAMMPS template input and data files from
-files.  Please note that the msi2lmp tool is very old and largely
+BIOVIA's Materials Studio files.  Please note that the msi2lmp tool is
-unmaintained, so it does not support all features of Materials Studio
+very old and largely unmaintained, so it does not support all features
-provided force field files, especially additions during the last decade.
+of Materials Studio provided force field files, especially additions
-You should watch the output carefully and compare results, where
+during the last decade.  You should watch the output carefully and
-possible.  See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS force
+compare results, where possible.  See :ref:`(Sun) <howto-Sun>` for a
-field.
+description of the COMPASS force field.
 
 These interaction styles listed below compute force field formulas that
 are consistent with the COMPASS force field.  See each command's
@@ -70,14 +191,21 @@ documentation for the formula it computes.
 
 * :doc:`special_bonds <special_bonds>` lj/coul 0 0 1
 
-DREIDING is a generic force field developed by the `Goddard group <http://www.wag.caltech.edu>`_ at Caltech and is useful for
+DREIDING
-predicting structures and dynamics of organic, biological and main-group
+--------
-inorganic molecules. The philosophy in DREIDING is to use general force
+
-constants and geometry parameters based on simple hybridization
+DREIDING is a generic force field developed by the `Goddard group
-considerations, rather than individual force constants and geometric
+<http://www.wag.caltech.edu>`_ at Caltech and is useful for predicting
-parameters that depend on the particular combinations of atoms involved
+structures and dynamics of organic, biological and main-group inorganic
-in the bond, angle, or torsion terms. DREIDING has an :doc:`explicit hydrogen bond term <pair_hbond_dreiding>` to describe interactions involving a
+molecules.  The philosophy in DREIDING is to use general force constants
-hydrogen atom on very electronegative atoms (N, O, F).
+and geometry parameters based on simple hybridization considerations,
+rather than individual force constants and geometric parameters that
+depend on the particular combinations of atoms involved in the bond,
+angle, or torsion terms.  DREIDING has an :doc:`explicit hydrogen bond
+term <pair_hbond_dreiding>` to describe interactions involving a
+hydrogen atom on very electronegative atoms (N, O, F).  Unlike CHARMM
+or AMBER, the DREIDING force field has not been parameterized for
+considering solvents (like water).
 
 See :ref:`(Mayo) <howto-Mayo>` for a description of the DREIDING force field
 
@@ -110,21 +238,31 @@ documentation for the formula it computes.
 
 ----------
 
+.. _Typelabel2:
+
+**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).
+
 .. _howto-MacKerell:
 
-**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al (1998).  J Phys Chem, 102, 3586 . https://doi.org/10.1021/jp973084f
-Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
 
 .. _howto-Cornell:
 
-**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
+**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman (1995).  JACS 117, 5179-5197. https://doi.org/10.1021/ja00124a002
-Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
+
+.. _howto-Steinbach:
+
+**(Steinbach)** Steinbach, Brooks (1994). J Comput Chem, 15, 667. https://doi.org/10.1002/jcc.540150702
+
+.. _howto-Brooks:
+
+**(Brooks)** Brooks, et al (2009). J Comput Chem, 30, 1545. https://onlinelibrary.wiley.com/doi/10.1002/jcc.21287
 
 .. _howto-Sun:
 
-**(Sun)** Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
+**(Sun)** Sun (1998). J. Phys. Chem. B, 102, 7338-7364. https://doi.org/10.1021/jp980939v
 
 .. _howto-Mayo:
 
-**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+**(Mayo)** Mayo, Olfason, Goddard III (1990). J Phys Chem, 94, 8897-8909. https://doi.org/10.1021/j100389a010
-(1990).
+

doc/src/Howto_chunk.rst

@@ -1,7 +1,7 @@
 Use chunks to calculate system properties
 =========================================
 
-In LAMMS, "chunks" are collections of atoms, as defined by the
+In LAMMPS, "chunks" are collections of atoms, as defined by the
 :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns
 each atom to a chunk ID (or to no chunk at all).  The number of chunks
 and the assignment of chunk IDs to atoms can be static or change over
@@ -148,14 +148,14 @@ Example calculations with chunks
 Here are examples using chunk commands to calculate various
 properties:
 
-(1) Average velocity in each of 1000 2d spatial bins:
+1. Average velocity in each of 1000 2d spatial bins:
 
 .. code-block:: LAMMPS
 
    compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
    fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
 
-(2) Temperature in each spatial bin, after subtracting a flow
+2. Temperature in each spatial bin, after subtracting a flow
 velocity:
 
 .. code-block:: LAMMPS
@@ -164,7 +164,7 @@ velocity:
    compute vbias all temp/profile 1 0 0 y 10
    fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
 
-(3) Center of mass of each molecule:
+3. Center of mass of each molecule:
 
 .. code-block:: LAMMPS
 
@@ -172,7 +172,7 @@ velocity:
    compute myChunk all com/chunk cc1
    fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
 
-(4) Total force on each molecule and ave/max across all molecules:
+4. Total force on each molecule and ave/max across all molecules:
 
 .. code-block:: LAMMPS
 
@@ -183,7 +183,7 @@ velocity:
    thermo 1000
    thermo_style custom step temp v_xave v_xmax
 
-(5) Histogram of cluster sizes:
+5. Histogram of cluster sizes:
 
 .. code-block:: LAMMPS
 
@@ -192,16 +192,16 @@ velocity:
    compute size all property/chunk cc1 count
    fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
 
-(6) An example for using a per-chunk value to apply per-atom forces to
+6. An example for using a per-chunk value to apply per-atom forces to
 compress individual polymer chains (molecules) in a mixture, is
 explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.
 
-(7) An example for using one set of per-chunk values for molecule
+7. An example for using one set of per-chunk values for molecule
 chunks, to create a second set of micelle-scale chunks (clustered
 molecules, due to hydrophobicity), is explained on the
 :doc:`compute reduce/chunk <compute_reduce_chunk>` command doc page.
 
-(8) An example for using one set of per-chunk values (dipole moment
+8. An example for using one set of per-chunk values (dipole moment
 vectors) for molecule chunks, spreading the values to each atom in
 each chunk, then defining a second set of chunks as spatial bins, and
 using the :doc:`fix ave/chunk <fix_ave_chunk>` command to calculate an

doc/src/Howto_cmake.rst

@@ -339,8 +339,6 @@ Some common LAMMPS specific variables
      - build LAMMPS with OpenMP support (default: ``on`` if compiler supports OpenMP fully, else ``off``)
    * - ``BUILD_TOOLS``
      - compile some additional executables from the ``tools`` folder (default: ``off``)
-   * - ``BUILD_LAMMPS_SHELL``
-     - compile the LAMMPS shell from the ``tools/lammps-shell`` folder (default: ``off``)
    * - ``BUILD_DOC``
      - include building the HTML format documentation for packaging/installing (default: ``off``)
    * - ``CMAKE_TUNE_FLAGS``

doc/src/Howto_lammps_gui.rst

@@ -1,11 +1,11 @@
-Using the LAMMPS GUI
+Using the LAMMPS-GUI
 ====================
 
-This document describes **LAMMPS GUI version 1.5**.
+This document describes **LAMMPS-GUI version 1.6**.
 
 -----
 
-LAMMPS GUI is a graphical text editor customized for editing LAMMPS
+LAMMPS-GUI is a graphical text editor customized for editing LAMMPS
 input files that is linked to the :ref:`LAMMPS library <lammps_c_api>`
 and thus can run LAMMPS directly using the contents of the editor's text
 buffer as input.  It can retrieve and display information from LAMMPS
@@ -16,58 +16,60 @@ to the online LAMMPS documentation for known LAMMPS commands and styles.
 
 .. note::
 
-   Pre-compiled, ready-to-use LAMMPS GUI executables for Linux (Ubuntu
+   Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux (Ubuntu
    20.04LTS or later and compatible), macOS (version 11 aka Big Sur or
    later), and Windows (version 10 or later) :ref:`are available
-   <lammps_gui_install>` for download.  They may be linked to a
+   <lammps_gui_install>` for download.  None-MPI LAMMPS executables of
-   development version of LAMMPS in case they need features not yet
+   the same LAMMPS version are included in these packages as well.  The
-   available in a released version. Serial LAMMPS executables of the
+   source code for the LAMMPS-GUI is included in the LAMMPS source code
-   same LAMMPS version are included as well.  The source code for the
+   distribution and can be found in the ``tools/lammps-gui`` folder.  It
-   LAMMPS GUI is included in the LAMMPS source code and can be found in
+   can be compiled alongside LAMMPS when :doc:`compiling with CMake
-   the ``tools/lammps-gui`` folder.  It can be compiled alongside LAMMPS
+   <Build_cmake>`.
-   when :doc:`compiling with CMake <Build_cmake>`.
 
-LAMMPS GUI tries to provide an experience similar to what people
+LAMMPS-GUI tries to provide an experience similar to what people
-traditionally would do to run LAMMPS using a command line window:
+traditionally would do to run LAMMPS using a command line window
+but just rolled into a single executable:
+
+- editing LAMMPS input files with a text editor
+- run LAMMPS on those input file with selected command line flags
+- use or extract data from the created files and visualize it with
+  either a molecular visualization program or a plotting program
 
-- editing inputs with a text editor
-- run LAMMPS on the input with selected command line flags
-- and then use or extract data from the created files and visualize it
 
 That procedure is quite effective for people proficient in using the
 command line, as that allows them to use tools for the individual steps
-which they are most comfortable with.  It is often required when running
+that they are most comfortable with.  It is often *required* to adopt
-LAMMPS on high-performance computing facilities.
+this workflow when running LAMMPS simulations on high-performance
+computing facilities.
 
-The main benefit of using the LAMMPS GUI application instead is that
+The main benefit of using the LAMMPS-GUI application instead is that
 many basic tasks can be done directly from the GUI without switching to
 a text console window or using external programs, let alone writing
 scripts to extract data from the generated output.  It also integrates
 well with graphical desktop environments.
 
-LAMMPS GUI thus makes it easier for beginners to get started running
+LAMMPS-GUI thus makes it easier for beginners to get started running
 simple LAMMPS simulations.  It is very suitable for tutorials on LAMMPS
 since you only need to learn how to use a single program for most tasks
 and thus time can be saved and people can focus on learning LAMMPS.  It
 is also designed to keep the barrier low when you decide to switch to a
 full featured, standalone programming editor and more sophisticated
-visualization and analysis tools and run LAMMPS from a command line.
+visualization and analysis tools, and run LAMMPS from the command line
+or a batch script.
 
 The following text provides a detailed tour of the features and
-functionality of the LAMMPS GUI.
+functionality of the LAMMPS-GUI.  Suggestions for new features and
-
+reports of bugs are always welcome.  You can use the :doc:`the same
-Suggestions for new features and reports of bugs are always welcome.
+channels as for LAMMPS itself <Errors_bugs>` for that purpose.
-You can use the :doc:`the same channels as for LAMMPS itself
-<Errors_bugs>` for that purpose.
 
 -----
 
-Main window
+Starting LAMMPS-GUI
------------
+-------------------
 
-When LAMMPS GUI starts, it will show a main window with either an
+When LAMMPS-GUI starts, it shows the main window, labeled *Editor*, with
-empty buffer or the contents of a loaded file. In the latter case it
+either an empty buffer or the contents of the file used as argument. In
-may look like the following:
+the latter case it may look like the following:
 
 .. image:: JPG/lammps-gui-main.png
    :align: center
@@ -80,32 +82,34 @@ the LAMMPS input file syntax.  The status bar shows the status of
 LAMMPS execution on the left (e.g. "Ready." when idle) and the current
 working directory on the right.  The name of the current file in the
 buffer is shown in the window title; the word `*modified*` is added if
-the buffer edits have not yet saved to a file.  The size of the main
+the buffer edits have not yet saved to a file.  The geometry of the main
-window will be stored when exiting and restored when starting again.
+window is stored when exiting and restored when starting again.
 
 Opening Files
 ^^^^^^^^^^^^^
 
-The LAMMPS GUI application will try to open the first command line
+The LAMMPS-GUI application tries to open the first command line argument
-argument as a LAMMPS input script, further arguments are ignored.
+as a LAMMPS input script, further arguments are ignored.  When no
-When no argument is given, LAMMPS GUI will start with an empty buffer.
+argument is given, LAMMPS-GUI starts with an empty buffer.  Files can
-Files can also be opened via the ``File`` menu or by drag-and-drop of
+also be opened via the ``File`` menu or by drag-and-drop of a file from
-a file from a graphical file manager into the editor window.  Only one
+a graphical file manager into the editor window.  Only one file can be
-file can be open at a time, so opening a new file with a filled buffer
+edited at a time, so opening a new file with a filled buffer closes that
-will close the buffer.  If the buffer has unsaved modifications, you
+buffer.  If the buffer has unsaved modifications, you are asked to
-will be asked to either cancel the operation, discard the changes, or
+either cancel the operation, discard the changes, or save them.  A
-save them.
+buffer with modifications can be saved any time from the "File" menu, by
+the keyboard shortcut `Ctrl-S` (`Command-S` on macOS), or by clicking on
+the "Save" button at the very left in the status bar.
 
 Running LAMMPS
 ^^^^^^^^^^^^^^
 
-From within the LAMMPS GUI main window LAMMPS can be started either from
+From within the LAMMPS-GUI main window LAMMPS can be started either from
 the ``Run`` menu using the ``Run LAMMPS from Editor Buffer`` entry, by
 the keyboard shortcut `Ctrl-Enter` (`Command-Enter` on macOS), or by
 clicking on the green "Run" button in the status bar.  All of these
-operations will cause LAMMPS to process the entire input script, which
+operations causes LAMMPS to process the entire input script in the
-may contain multiple :doc:`run <run>` or :doc:`minimize <minimize>`
+editor buffer, which may contain multiple :doc:`run <run>` or
-commands.
+:doc:`minimize <minimize>` commands.
 
 LAMMPS runs in a separate thread, so the GUI stays responsive and is
 able to interact with the running calculation and access data it
@@ -128,33 +132,30 @@ before LAMMPS can be run from a file.
 
 While LAMMPS is running, the contents of the status bar change.  On
 the left side there is a text indicating that LAMMPS is running, which
-will also show the number of active threads, if thread-parallel
+also indicates the number of active threads, when thread-parallel
 acceleration was selected in the ``Preferences`` dialog.  On the right
 side, a progress bar is shown that displays the estimated progress for
-the current :doc:`run command <run>`.
+the current :doc:`run <run>` or :doc:`minimize <minimize>` command.
 
-Also, the line number of the currently executed command will be
+Also, the line number of the currently executed command is highlighted
-highlighted in green.
+in green.
-
-.. image:: JPG/lammps-gui-run-highlight.png
-   :align: center
-   :scale: 75%
 
 If an error occurs (in the example below the command :doc:`label
 <label>` was incorrectly capitalized as "Label"), an error message
-dialog will be shown and the line of the input which triggered the
+dialog is shown and the line of the input which triggered the error is
-error will be highlighted.  The state of LAMMPS in the status bar will
+highlighted.  The state of LAMMPS in the status bar is set to "Failed."
-be set to "Failed." instead of "Ready."
+instead of "Ready."
 
 .. image:: JPG/lammps-gui-run-error.png
    :align: center
    :scale: 75%
 
-Up to three additional windows will open during a run:
+Up to three additional windows may open during a run:
 
-- a log window with the captured screen output
+- an *Output* window with the captured screen output from LAMMPS
-- a chart window with a line graph created from the thermodynamic output of the run
+- a *Charts* window with a line graph created from thermodynamic output of the run
-- a slide show window with images created by a :doc:`dump image command <dump_image>`
+- a *Slide Show* window with images created by a :doc:`dump image command <dump_image>`
+  in the input
 
 More information on those windows and how to adjust their behavior and
 contents is given below.
@@ -171,55 +172,68 @@ This is equivalent to the input script command :doc:`timer timeout 0
 interface.  Please see the corresponding documentation pages to
 understand the implications of this operation.
 
-Log Window
+Output Window
-----------
+-------------
 
-By default, when starting a run, a "Log Window" will open that displays
+By default, when starting a run, an *Output* window opens that displays
-the current screen output of the LAMMPS calculation, that would normally
+the screen output of the running LAMMPS calculation, as shown below.
-be seen in the command line window, as shown below.
+This text would normally be seen in the command line window.
 
 .. image:: JPG/lammps-gui-log.png
    :align: center
    :scale: 50%
 
-LAMMPS GUI captures the screen output as it is generated and updates
+LAMMPS-GUI captures the screen output from LAMMPS as it is generated and
-the log window regularly during a run.
+updates the *Output* window regularly during a run.
 
-By default, the log window will be replaced each time a run is started.
+By default, the *Output* window is replaced each time a run is started.
 The runs are counted and the run number for the current run is displayed
-in the window title.  It is possible to change the behavior of LAMMPS
+in the window title.  It is possible to change the behavior of
-GUI in the preferences dialog to create a *new* log window for every run
+LAMMPS-GUI in the preferences dialog to create a *new* *Output* window
-or to not show the current log window.  It is also possible to show or
+for every run or to not show the current *Output* window.  It is also
-hide the *current* log window from the ``View`` menu.
+possible to show or hide the *current* *Output* window from the ``View``
+menu.
 
-The text in the log window is read-only and cannot be modified, but
+The text in the *Output* window is read-only and cannot be modified, but
 keyboard shortcuts to select and copy all or parts of the text can be
 used to transfer text to another program. Also, the keyboard shortcut
-`Ctrl-S` (`Command-S` on macOS) is available to save the log buffer to a
+`Ctrl-S` (`Command-S` on macOS) is available to save the *Output* buffer to a
 file.  The "Select All" and "Copy" functions, as well as a "Save Log to
 File" option are also available from a context menu by clicking with the
-right mouse button into the log window text area.
+right mouse button into the *Output* window text area.
 
-Chart Window
+.. image:: JPG/lammps-gui-yaml.png
-------------
-
-By default, when starting a run, a "Chart Window" will open that
-displays a plot of thermodynamic output of the LAMMPS calculation as
-shown below.
-
-.. image:: JPG/lammps-gui-chart.png
    :align: center
    :scale: 50%
 
+.. versionadded:: 1.6
+
+Should the *Output* window contain embedded YAML format text (see above for a
+demonstration), for example from using :doc:`thermo_style yaml
+<thermo_style>` or :doc:`thermo_modify line yaml <thermo_modify>`, the
+keyboard shortcut `Ctrl-Y` (`Command-Y` on macOS) is available to save
+only the YAML parts to a file.  This option is also available from a
+context menu by clicking with the right mouse button into the *Output* window
+text area.
+
+Charts Window
+-------------
+
+By default, when starting a run, a *Charts* window opens that displays a
+plot of thermodynamic output of the LAMMPS calculation as shown below.
+
+.. image:: JPG/lammps-gui-chart.png
+   :align: center
+   :scale: 33%
+
 The drop down menu on the top right allows selection of different
 properties that are computed and written to thermo output.  Only one
-property can be shown at a time.  The plots will be updated with new
+property can be shown at a time.  The plots are updated with new data as
-data as the run progresses, so they can be used to visually monitor the
+the run progresses, so they can be used to visually monitor the
-evolution of available properties.  The window title will show the
+evolution of available properties.  The window title shows the current
-current run number that this chart window corresponds to.  Same as
+run number that this chart window corresponds to.  Same as for the
-explained for the log window above, by default, the chart window will
+*Output* window, the chart window is replaced on each new run, but the
-be replaced on each new run, but the behavior can be changed in the
+behavior can be changed in the preferences dialog.
-preferences dialog.
 
 From the ``File`` menu on the top left, it is possible to save an image
 of the currently displayed plot or export the data in either plain text
@@ -229,19 +243,20 @@ columns (for use by plotting tools like `gnuplot
 be imported for further processing with Microsoft Excel or `pandas
 <https://pandas.pydata.org/>`_
 
-Thermo output data from successive run commands in the input script will
+Thermo output data from successive run commands in the input script is
-be combined into a single data set unless the format, number, or names
+combined into a single data set unless the format, number, or names of
-of output columns are changed with a :doc:`thermo_style <thermo_style>`
+output columns are changed with a :doc:`thermo_style <thermo_style>` or
-or a :doc:`thermo_modify <thermo_modify>` command, or the current time
+a :doc:`thermo_modify <thermo_modify>` command, or the current time step
-step is reset with :doc:`reset_timestep <reset_timestep>`, or if a
+is reset with :doc:`reset_timestep <reset_timestep>`, or if a
 :doc:`clear <clear>` command is issued.
 
 Image Slide Show
 ----------------
 
 By default, if the LAMMPS input contains a :doc:`dump image
-<dump_image>` command, a "Slide Show" window will open which loads and
+<dump_image>` command, a "Slide Show" window opens which loads and
-displays the images created by LAMMPS as they are written.
+displays the images created by LAMMPS as they are written.  This is a
+convenient way to visually monitor the progress of the simulation.
 
 .. image:: JPG/lammps-gui-slideshow.png
    :align: center
@@ -250,9 +265,17 @@ displays the images created by LAMMPS as they are written.
 The various buttons at the bottom right of the window allow single
 stepping through the sequence of images or playing an animation (as a
 continuous loop or once from first to last).  It is also possible to
-zoom in or zoom out of the displayed images, and to export the slide
+zoom in or zoom out of the displayed images. The button on the very
-show animation to a movie file, if `ffmpeg <https://ffmpeg.org/>`_ is
+left triggers an export of the slide show animation to a movie file,
-installed.
+provided the `FFmpeg program <https://ffmpeg.org/>`_ is installed.
+
+.. versionadded:: 1.6
+
+When clicking on the "garbage can" icon, all image files of the slide
+show will be deleted.  Since their number can be large for long
+simulations, this option enables to safely and quickly clean up the
+clutter caused in the working directory by those image files without
+risk of deleting other files by accident when using wildcards.
 
 Variable Info
 -------------
@@ -260,23 +283,22 @@ Variable Info
 During a run, it may be of interest to monitor the value of input script
 variables, for example to monitor the progress of loops.  This can be
 done by enabling the "Variables Window" in the ``View`` menu or by using
-the `Ctrl-Shift-W` keyboard shortcut.  This will show info similar to
+the `Ctrl-Shift-W` keyboard shortcut.  This shows info similar to the
-the :doc:`info variables <info>` command in a separate window as shown
+:doc:`info variables <info>` command in a separate window as shown
 below.
 
 .. image:: JPG/lammps-gui-variable-info.png
    :align: center
    :scale: 75%
 
-Like the log and chart windows, its content is continuously updated
+Like for the *Output* and *Charts* windows, its content is continuously
-during a run.  It will show "(none)" if there are no variables
+updated during a run.  It will show "(none)" if there are no variables
 defined.  Note that it is also possible to *set* :doc:`index style
 variables <variable>`, that would normally be set via command line
 flags, via the "Set Variables..." dialog from the ``Run`` menu.
-LAMMPS GUI will automatically set the variable "gui_run" to the
+LAMMPS-GUI automatically defines the variable "gui_run" to the current
-current value of the run counter.  That way it would be possible
+value of the run counter.  That way it is possible to automatically
-to automatically record a log for each run attempt by using the
+record a separate log for each run attempt by using the command
-command
 
 .. code-block:: LAMMPS
 
@@ -285,26 +307,34 @@ command
 at the beginning of an input file. That would record logs to files
 ``logfile-1.txt``, ``logfile-2.txt``, and so on for successive runs.
 
-Viewing Snapshot Images
+Snapshot Image Viewer
------------------------
+---------------------
 
 By selecting the ``Create Image`` entry in the ``Run`` menu, or by
 hitting the `Ctrl-I` (`Command-I` on macOS) keyboard shortcut, or by
-clicking on the "palette" button in the status bar, LAMMPS GUI will send
+clicking on the "palette" button in the status bar of the *Editor*
-a custom :doc:`write_dump image <dump_image>` command to LAMMPS and read
+window, LAMMPS-GUI sends a custom :doc:`write_dump image <dump_image>`
-the resulting snapshot image with the current state of the system into
+command to LAMMPS and reads back the resulting snapshot image with the
-an image viewer window.  This functionality is not available *during* an
+current state of the system into an image viewer.  This functionality is
-ongoing run.  When LAMMPS is not yet initialized, LAMMPS GUI will try to
+*not* available *during* an ongoing run.  In case LAMMPS is not yet
-identify the line with the first run or minimize command and execute all
+initialized, LAMMPS-GUI tries to identify the line with the first run or
-command up to that line from the input buffer and then add a "run 0"
+minimize command and execute all commands from the input buffer up to
-command.  This will initialize the system so an image of the initial
+that line, and then executes a "run 0" command.  This initializes the
-state of the system can be rendered.  If there was an error, the
+system so an image of the initial state of the system can be rendered.
-snapshot image viewer will not appear.
+If there was an error in that process, the snapshot image viewer does
+not appear.
 
-When possible, LAMMPS GUI will try to detect which elements the atoms
+When possible, LAMMPS-GUI tries to detect which elements the atoms
-correspond to (via their mass) and then colorize them in the image
+correspond to (via their mass) and then colorize them in the image and
-accordingly.  Otherwise the default predefined sequence of colors is
+set their atom diameters accordingly.  If this is not possible, for
-assigned to the different atom types.
+instance when using reduced (= 'lj') :doc:`units <units>`, then
+LAMMPS-GUI will check the current pair style and if it is a
+Lennard-Jones type potential, it will extract the *sigma* parameter
+for each atom type and assign atom diameters from those numbers.
+
+Otherwise the default sequence of colors of the :doc:`dump image
+<dump_image>` command is assigned to the different atom types and the
+diameters are all the same.
 
 .. image:: JPG/lammps-gui-image.png
    :align: center
@@ -314,33 +344,43 @@ The default image size, some default image quality settings, the view
 style and some colors can be changed in the ``Preferences`` dialog
 window.  From the image viewer window further adjustments can be made:
 actual image size, high-quality (SSAO) rendering, anti-aliasing, view
-style, display of box or axes, zoom factor.  The view of the system
+style, display of box or axes, zoom factor.  The view of the system can
-can be rotated horizontally and vertically.  It is also possible to
+be rotated horizontally and vertically.  It is also possible to only
-only display the atoms within a group defined in the input script
+display the atoms within a group defined in the input script (default is
-(default is "all").  After each change, the image is rendered again
+"all").  After each change, the image is rendered again and the display
-and the display updated.  The small palette icon on the top left will
+updated.  The small palette icon on the top left is colored while LAMMPS
-be colored while LAMMPS is running to render the new image; it will be
+is running to render the new image; it is grayed out when LAMMPS is
-grayed out when it is finished.  When there are many atoms to render
+finished.  When there are many atoms to render and high quality images
-and high quality images with anti-aliasing are requested, re-rendering
+with anti-aliasing are requested, re-rendering may take several seconds.
-may take several seconds.  From the ``File`` menu of the image window,
+From the ``File`` menu of the image window, the current image can be
-the current image can be saved to a file or copied into the
+saved to a file (keyboard shortcut `Ctrl-S`) or copied to the clipboard
-cut-n-paste buffer for pasting into another application.
+(keyboard shortcut `Ctrl-C`) for pasting the image into another
+application.
 
-Editor Functions
+.. versionadded:: 1.6
-----------------
 
-The editor has most of the usual functionality that similar programs
+From the ``File`` menu it is also possible to copy the current
-have: text selection via mouse or with cursor moves while holding the
+:doc:`dump image <dump_image>` and :doc:`dump_modify <dump_image>`
-Shift key, Cut (`Ctrl-X`), Copy (`Ctrl-C`), Paste (`Ctrl-V`), Undo
+commands to the clipboard so they can be pasted into a LAMMPS input file
-(`Ctrl-Z`), Redo (`Ctrl-Shift-Z`), Select All (`Ctrl-A`).  When trying
+so that the visualization settings of the snapshot image can be repeated
-to exit the editor with a modified buffer, a dialog will pop up asking
+for the entire simulation (and thus be repeated in the slide show
-whether to cancel the exit operation, or to save or not save the buffer
+viewer). This feature has the keyboard shortcut `Ctrl-D`.
-contents to a file.
+
+Editor Window
+-------------
+
+The *Editor* window of LAMMPS-GUI has most of the usual functionality
+that similar programs have: text selection via mouse or with cursor
+moves while holding the Shift key, Cut (`Ctrl-X`), Copy (`Ctrl-C`),
+Paste (`Ctrl-V`), Undo (`Ctrl-Z`), Redo (`Ctrl-Shift-Z`), Select All
+(`Ctrl-A`).  When trying to exit the editor with a modified buffer, a
+dialog will pop up asking whether to cancel the exit operation, or to
+save or not save the buffer contents to a file.
 
 Context Specific Word Completion
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-By default, LAMMPS GUI will display a small pop-up frame with possible
+By default, LAMMPS-GUI displays a small pop-up frame with possible
 choices for LAMMPS input script commands or styles after 2 characters of
 a word have been typed.
 
@@ -354,10 +394,10 @@ by clicking on the entry with the mouse.  The automatic completion
 pop-up can be disabled in the ``Preferences`` dialog, but the completion
 can still be requested manually by either hitting the 'Shift-TAB' key or
 by right-clicking with the mouse and selecting the option from the
-context menu.  Most of the completion information is taken from the
+context menu.  Most of the completion information is retrieved from the
-LAMMPS instance and thus it will be adjusted to only show available
+active LAMMPS instance and thus it shows only available options that
-options that have been enabled while compiling LAMMPS. That, however,
+have been enabled when compiling LAMMPS. That list, however, excludes
-excludes accelerated styles and commands; for improved clarity, only the
+accelerated styles and commands; for improved clarity, only the
 non-suffix version of styles are shown.
 
 Line Reformatting
@@ -369,8 +409,8 @@ whitespace padding to commands, type specifiers, IDs and names.  This
 reformatting is performed by default when hitting the 'Enter' key to
 start a new line.  This feature can be turned on or off in the
 ``Preferences`` dialog, but it can still be manually performed by
-hitting the 'TAB' key.  The amount of padding can also be changed in the
+hitting the 'TAB' key.  The amount of padding can be adjusted in the
-``Preferences`` dialog.
+``Preferences`` dialog for the *Editor*.
 
 Internally this functionality is achieved by splitting the line into
 "words" and then putting it back together with padding added where the
@@ -379,17 +419,26 @@ context can be detected; otherwise a single space is used between words.
 Context Specific Help
 ^^^^^^^^^^^^^^^^^^^^^
 
-.. image:: JPG/lammps-gui-popup-help.png
+.. |gui-popup1| image:: JPG/lammps-gui-popup-help.png
-   :align: center
+   :width: 48%
-   :scale: 50%
 
-A unique feature of the LAMMPS GUI is the option to look up the
+.. |gui-popup2| image:: JPG/lammps-gui-popup-view.png
+   :width: 48%
+
+|gui-popup1|  |gui-popup2|
+
+A unique feature of the LAMMPS-GUI is the option to look up the
 documentation for the command in the current line.  This can be done by
 either clicking the right mouse button or by using the `Ctrl-?` keyboard
-shortcut.  When clicking the mouse there are additional entries in the
+shortcut.  When using the mouse, there are additional entries in the
-context menu that will open the corresponding documentation page in the
+context menu that open the corresponding documentation page in the
-online LAMMPS documentation.  When using the keyboard, the first of
+online LAMMPS documentation in a web browser window.  When using the
-those entries will be chosen directly.
+keyboard, the first of those entries is chosen.
+
+If the word under the cursor is a file, then additionally the context
+menu has an entry to open the file in a read-only text viewer window.
+This is a convenient way to view the contents of files that are
+referenced in the input.
 
 Menu
 ----
@@ -397,9 +446,9 @@ Menu
 The menu bar has entries ``File``, ``Edit``, ``Run``, ``View``, and
 ``About``.  Instead of using the mouse to click on them, the individual
 menus can also be activated by hitting the `Alt` key together with the
-corresponding underlined letter, that is `Alt-F` will activate the
+corresponding underlined letter, that is `Alt-F` activates the
 ``File`` menu.  For the corresponding activated sub-menus, the key
-corresponding the underlined letters can again be used to select entries
+corresponding the underlined letters can be used to select entries
 instead of using the mouse.
 
 File
@@ -407,19 +456,22 @@ File
 
 The ``File`` menu offers the usual options:
 
-- ``New`` will clear the current buffer and reset the file name to ``*unknown*``
+- ``New`` clears the current buffer and resets the file name to ``*unknown*``
-- ``Open`` will open a dialog to select a new file
+- ``Open`` opens a dialog to select a new file for editing in the *Editor*
-- ``Save`` will save the current file; if the file name is ``*unknown*``
+- ``View`` opens a dialog to select a file for viewing in a *separate* window (read-only)
+- ``Save`` saves the current file; if the file name is ``*unknown*``
   a dialog will open to select a new file name
-- ``Save As`` will open a dialog to select and new file name and save
+- ``Save As`` opens a dialog to select and new file name (and folder, if
-  the buffer to it
+  desired) and saves the buffer to it.  Writing the buffer to a
-- ``Quit`` will exit LAMMPS GUI. If there are unsaved changes, a dialog
+  different folder will also switch the current working directory to
-  will appear to either cancel the operation, or to save or not save the
+  that folder.
-  edited file.
+- ``Quit`` exits LAMMPS-GUI. If there are unsaved changes, a dialog will
+  appear to either cancel the operation, or to save, or to not save the
+  modified buffer.
 
-In addition, up to 5 recent file names will be listed after the
+In addition, up to 5 recent file names will be listed after the ``Open``
-``Open`` entry that allows re-opening recent files.  This list is
+entry that allows re-opening recently opened files.  This list is stored
-stored when quitting and recovered when starting again.
+when quitting and recovered when starting again.
 
 Edit
 ^^^^
@@ -427,19 +479,20 @@ Edit
 The ``Edit`` menu offers the usual editor functions like ``Undo``,
 ``Redo``, ``Cut``, ``Copy``, ``Paste``.  It can also open a
 ``Preferences`` dialog (keyboard shortcut `Ctrl-P`) and allows deletion
-of all stored preferences so they will be reset to default values.
+of all stored preferences and settings, so they are reset to their
+default values.
 
 Run
 ^^^
 
-The ``Run`` menu has options to start and stop a LAMMPS process.
+The ``Run`` menu has options to start and stop a LAMMPS process.  Rather
-Rather than calling the LAMMPS executable as a separate executable,
+than calling the LAMMPS executable as a separate executable, the
-the LAMMPS GUI is linked to the LAMMPS library and thus can run LAMMPS
+LAMMPS-GUI is linked to the LAMMPS library and thus can run LAMMPS
-internally through the :ref:`LAMMPS C-library interface
+internally through the :ref:`LAMMPS C-library interface <lammps_c_api>`
-<lammps_c_api>`.
+in a separate thread.
 
 Specifically, a LAMMPS instance will be created by calling
-:cpp:func:`lammps_open_no_mpi`.  The buffer contents then executed by
+:cpp:func:`lammps_open_no_mpi`.  The buffer contents are then executed by
 calling :cpp:func:`lammps_commands_string`.  Certain commands and
 features are only available after a LAMMPS instance is created.  Its
 presence is indicated by a small LAMMPS ``L`` logo in the status bar
@@ -449,16 +502,16 @@ reading the file.  This is mainly provided as a fallback option in
 case the input uses some feature that is not available when running
 from a string buffer.
 
-The LAMMPS calculation will be run in a concurrent thread so that the
+The LAMMPS calculations are run in a concurrent thread so that the GUI
-GUI can stay responsive and be updated during the run.  This can be
+can stay responsive and be updated during the run.  The GUI can retrieve
-used to tell the running LAMMPS instance to stop at the next timestep.
+data from the running LAMMPS instance and tell it to stop at the next
-The ``Stop LAMMPS`` entry will do this by calling
+timestep.  The ``Stop LAMMPS`` entry will do this by calling the
-:cpp:func:`lammps_force_timeout`, which is equivalent to a :doc:`timer
+:cpp:func:`lammps_force_timeout` library function, which is equivalent
-timeout 0 <timer>` command.
+to a :doc:`timer timeout 0 <timer>` command.
 
-The ``Set Variables...`` entry will open a dialog box where
+The ``Set Variables...`` entry opens a dialog box where
 :doc:`index style variables <variable>` can be set. Those variables
-will be passed to the LAMMPS instance when it is created and are thus
+are passed to the LAMMPS instance when it is created and are thus
 set *before* a run is started.
 
 .. image:: JPG/lammps-gui-variables.png
@@ -478,12 +531,12 @@ in an ``Image Viewer`` window.
 
 The ``View in OVITO`` entry will launch `OVITO <https://ovito.org>`_
 with a :doc:`data file <write_data>` containing the current state of
-the system.  This option is only available if the LAMMPS GUI can find
+the system.  This option is only available if the LAMMPS-GUI can find
 the OVITO executable in the system path.
 
 The ``View in VMD`` entry will launch VMD with a :doc:`data file
 <write_data>` containing the current state of the system.  This option
-is only available if the LAMMPS GUI can find the VMD executable in the
+is only available if the LAMMPS-GUI can find the VMD executable in the
 system path.
 
 View
@@ -498,14 +551,14 @@ About
 ^^^^^
 
 The ``About`` menu finally offers a couple of dialog windows and an
-option to launch the LAMMPS online documentation in a web browser.
+option to launch the LAMMPS online documentation in a web browser.  The
-The ``About LAMMPS`` entry displays a dialog with a summary of the
+``About LAMMPS-GUI`` entry displays a dialog with a summary of the
 configuration settings of the LAMMPS library in use and the version
-number of LAMMPS GUI itself.  The ``Quick Help`` displays a dialog
+number of LAMMPS-GUI itself.  The ``Quick Help`` displays a dialog with
-with a minimal description of LAMMPS GUI.  The ``LAMMPS GUI Howto``
+a minimal description of LAMMPS-GUI.  The ``LAMMPS-GUI Howto`` entry
-entry will open this documentation page from the online documentation
+will open this documentation page from the online documentation in a web
-in a web browser window.  The ``LAMMPS Manual`` entry will open the
+browser window.  The ``LAMMPS Manual`` entry will open the main page of
-main page of the LAMMPS documentation in the web browser.
+the LAMMPS online documentation in a web browser window.
 
 -----
 
@@ -513,7 +566,7 @@ Preferences
 -----------
 
 The ``Preferences`` dialog allows customization of the behavior and
-look of the LAMMPS GUI application.  The settings are grouped and each
+look of the LAMMPS-GUI application.  The settings are grouped and each
 group is displayed within a tab.
 
 .. |guiprefs1| image:: JPG/lammps-gui-prefs-general.png
@@ -534,9 +587,9 @@ General Settings:
 ^^^^^^^^^^^^^^^^^
 
 - *Echo input to log:* when checked, all input commands, including
-  variable expansions, will be echoed to the log window. This is
+  variable expansions, are echoed to the *Output* window. This is
   equivalent to using `-echo screen` at the command line.  There is no
-  log *file* produced by default, since LAMMPS GUI uses `-log none`.
+  log *file* produced by default, since LAMMPS-GUI uses `-log none`.
 - *Include citation details:* when checked full citation info will be
   included to the log window.  This is equivalent to using `-cite
   screen` on the command line.
@@ -558,12 +611,12 @@ General Settings:
   chart window will be replaced when a new snapshot image is requested,
   otherwise each command will create a new image window.
 - *Path to LAMMPS Shared Library File:* this option is only visible
-  when LAMMPS GUI was compiled to load the LAMMPS library at run time
+  when LAMMPS-GUI was compiled to load the LAMMPS library at run time
   instead of being linked to it directly.  With the ``Browse..`` button
   or by changing the text, a different shared library file with a
   different compilation of LAMMPS with different settings or from a
   different version can be loaded.  After this setting was changed,
-  LAMMPS GUI needs to be re-launched.
+  LAMMPS-GUI needs to be re-launched.
 - *Select Default Font:* Opens a font selection dialog where the type
   and size for the default font (used for everything but the editor and
   log) of the application can be set.
@@ -571,11 +624,12 @@ General Settings:
   size for the text editor and log font of the application can be set.
 - *GUI update interval:* Allows to set the time interval between GUI
   and data updates during a LAMMPS run in milliseconds. The default is
-  to update the GUI every 100 milliseconds. This is good for most cases.
+  to update the GUI every 10 milliseconds. This is good for most cases.
-  For LAMMPS runs that run very fast, however, data may be missed and
+  For LAMMPS runs that run *very* fast, however, data may be missed and
   through lowering this interval, this can be corrected. However, this
   will make the GUI use more resources, which may be a problem on some
-  computers with slower CPUs. The default value is 100 milliseconds.
+  computers with slower CPUs and a small number of CPU cores. This
+  setting may be changed to a value between 1 and 1000 milliseconds.
 
 Accelerators:
 ^^^^^^^^^^^^^
@@ -648,48 +702,54 @@ available (On macOS use the Command key instead of Ctrl/Control).
      - Redo edit
      - Ctrl+/
      - Stop Active Run
-   * - Ctrl+S
+   * - Ctrl+Shift+F
-     - Save File
+     - View File
      - Ctrl+C
      - Copy text
      - Ctrl+Shift+V
      - Set Variables
-   * - Ctrl+Shift+S
+   * - Ctrl+S
-     - Save File As
+     - Save File
      - Ctrl+X
      - Cut text
      - Ctrl+I
      - Snapshot Image
-   * - Ctrl+Q
+   * - Ctrl+Shift+S
-     - Quit Application
+     - Save File As
      - Ctrl+V
      - Paste text
      - Ctrl+L
      - Slide Show
-   * - Ctrl+W
+   * - Ctrl+Q
-     - Close Window
+     - Quit Application
      - Ctrl+A
      - Select All
      - Ctrl+P
      - Preferences
-   * - Ctrl+Shift+A
+   * - Ctrl+W
-     - About LAMMPS
+     - Close Window
      - Ctrl+Shift+H
      - Quick Help
      - Ctrl+Shift+G
-     - LAMMPS GUI Howto
+     - LAMMPS-GUI Howto
-   * - Ctrl+Shift+M
+   * - Ctrl+Shift+A
-     - LAMMPS Manual
+     - About LAMMPS
      - Ctrl+?
      - Context Help
      - Ctrl+Shift+W
      - Show Variables
-   * - Ctrl+Shift+Enter
+   * - Ctrl+Shift+M
-     - Run File
+     - LAMMPS Manual
      - TAB
      - Reformat line
      - Shift+TAB
      - Show Completions
+   * - Ctrl+Shift+Enter
+     - Run File
+     -
+     -
+     -
+     -
 
 Further editing keybindings `are documented with the Qt documentation
 <https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_.  In

doc/src/Howto_rheo.rst

@@ -0,0 +1,116 @@
+Reproducing hydrodynamics and elastic objects (RHEO)
+====================================================
+
+The RHEO package is a hybrid implementation of smoothed particle
+hydrodynamics (SPH) for fluid flow, which can couple to the :doc:`BPM package
+<Howto_bpm>` to model solid elements. RHEO combines these methods to enable
+mesh-free modeling of multi-phase material systems. Its SPH solver supports
+many advanced options including reproducing kernels, particle shifting, free
+surface identification, and solid surface reconstruction. To model fluid-solid
+systems, the status of particles can dynamically change between a fluid and
+solid state, e.g. during melting/solidification, which determines how they
+interact and their physical behavior. The package is designed with modularity
+in mind, so one can easily turn various features on/off, adjust physical
+details of the system, or develop new capabilities. For instance, the numerics
+associated with calculating gradients, reproducing kernels, etc. are separated
+into distinct classes to simplify the development of new integration schemes
+which can call these calculations. Additional numerical details can be found in
+:ref:`(Palermo) <howto_rheo_palermo>` and
+:ref:`(Clemmer) <howto_rheo_clemmer>`.
+
+Note, if you simply want to run a traditional SPH simulation, the :ref:`SPH package
+<PKG-SPH>` package is likely better suited for your application. It has fewer advanced
+features and therefore benefits from improved performance. The :ref:`MACHDYN
+<PKG-MACHDYN>` package for solids may also be relevant for fluid-solid problems.
+
+----------
+
+At the core of the package is :doc:`fix rheo <fix_rheo>` which integrates
+particle trajectories and controls many optional features (e.g. the use
+of reproducing kernels). In conjunction to fix rheo, one must specify an
+instance of :doc:`fix rheo/pressure <fix_rheo_pressure>` and
+:doc:`fix rheo/viscosity <fix_rheo_viscosity>` to define a pressure equation
+of state and viscosity model, respectively. Optionally, one can model
+a heat equation with :doc:`fix rheo/thermal <fix_rheo_thermal>`, which also
+allows the user to specify equations for a particle's thermal conductivity,
+specific heat, latent heat, and melting temperature. The ordering of these
+fixes in an an input script matters. Fix rheo must be defined prior to all
+other RHEO fixes.
+
+Typically, RHEO requires atom style rheo. In addition to typical atom
+properties like positions and forces, particles store a local density,
+viscosity, pressure, and status. If thermal evolution is modeled, one must
+use atom style rheo/thermal which also includes a local energy, temperature, and
+conductivity. Note that the temperature is always derived from the energy.
+This implies the *temperature* attribute of :doc:`the set command <set>` does not
+affect particles. Instead, one should use the *sph/e* attribute.
+
+The status variable uses bit-masking to track various properties of a particle
+such as its current state of matter (fluid or solid) and its location relative
+to a surface. Some of these properties (and others) can be accessed using
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`. The *status*
+attribute in :doc:`the set command <set>` only allows control over the first bit
+which sets the state of matter, 0 is fluid and 1 is solid.
+
+Fluid interactions, including pressure forces, viscous forces, and heat exchange,
+are calculated using :doc:`pair rheo <pair_rheo>`. Unlike typical pair styles,
+pair rheo ignores the :doc:`special bond <special_bonds>` settings. Instead,
+it determines whether to calculate forces based on the status of particles: e.g.,
+hydrodynamic forces are only calculated if a fluid particle is involved.
+
+----------
+
+To model elastic objects, there are currently two mechanisms in RHEO, one designed
+for bulk solid bodies and the other for thin shells. Both mechanisms rely on
+introducing bonded forces between particles and therefore require a hybrid of atom
+style bond and rheo (or rheo/thermal).
+
+To create an elastic solid body, one has to (a) change the status of constituent
+particles to solid (e.g. with the :doc:`set <set>` command), (b) create bpm
+bonds between the particles (see the :doc:`bpm howto <Howto_bpm>` page for
+more details), and (c) use :doc:`pair rheo/solid <pair_rheo_solid>` to
+apply repulsive contact forces between distinct solid bodies. Akin to pair rheo,
+pair rheo/solid considers a particles fluid/solid phase to determine whether to
+apply forces. However, unlike pair rheo, pair rheo/solid does obey special bond
+settings such that contact forces do not have to be calculated between two bonded
+solid particles in the same elastic body.
+
+In systems with thermal evolution, fix rheo/thermal can optionally set a
+melting/solidification temperature allowing particles to dynamically swap their
+state between fluid and solid when the temperature exceeds or drops below the
+critical temperature, respectively. Using the *react* option, one can specify a maximum
+bond length and a bond type. Then, when solidifying, particles will search their
+local neighbors and automatically create bonds with any neighboring solid particles
+in range. For BPM bond styles, bonds will then use the immediate position of the two
+particles to calculate a reference state. When melting, particles will delete any
+bonds of the specified type when reverting to a fluid state. Special bonds are updated
+as bonds are created/broken.
+
+The other option for elastic objects is an elastic shell that is nominally much
+thinner than a particle diameter, e.g. a oxide skin which gradually forms over time
+on the surface of a fluid. Currently, this is implemented using
+:doc:`fix rheo/oxidation <fix_rheo_oxidation>` and bond style
+:doc:`rheo/shell <bond_rheo_shell>`. Essentially, fix rheo/oxidation creates candidate
+bonds of a specified type between surface fluid particles within a specified distance.
+a newly created rheo/shell bond will then start a timer. While the timer is counting
+down, the bond will delete itself if particles move too far apart or move away from the
+surface. However, if the timer reaches a user-defined threshold, then the bond will
+activate and apply additional forces to the fluid particles. Bond style rheo/shell
+then operates very similarly to a BPM bond style, storing a reference length and
+breaking if stretched too far. Unlike the above method, this option does not remove
+the underlying fluid interactions (although particle shifting is turned off) and does
+not modify special bond settings of particles.
+
+While these two options are not expected to be appropriate for every system,
+either framework can be modified to create more suitable models (e.g. by changing the
+criteria for creating/deleting a bond or altering force calculations).
+
+----------
+
+.. _howto_rheo_palermo:
+
+**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.
+
+.. _howto_rheo_clemmer:
+
+**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

doc/src/Install_linux.rst

@@ -35,11 +35,11 @@ packages listed below), they do not depend on any installed software and
 thus should run on *any* 64-bit x86 machine with *any* Linux version.
 
 These executable include most of the available packages and multi-thread
-parallelization (via INTEL, KOKKOS, or OPENMP package).  They are **not**
+parallelization (via INTEL, KOKKOS, or OPENMP package).  They are
-compatible with MPI.  Several of the LAMMPS tools executables (e.g. ``msi2lmp``)
+**not** compatible with MPI.  Several of the LAMMPS tools executables
-and the ``lammps-shell`` program are included as well.  Because of the
+(e.g. ``msi2lmp``) are included as well.  Because of the static linkage,
-static linkage, there is no ``liblammps.so`` library file and thus also the
+there is no ``liblammps.so`` library file and thus also the LAMMPS
-LAMMPS python module, which depends on it, is not included.
+python module, which depends on it, is not included.
 
 The compressed tar archives available for download have names following
 the pattern ``lammps-linux-x86_64-<version>.tar.gz`` and will all unpack

doc/src/Library_properties.rst

@@ -13,6 +13,8 @@ This section documents the following functions:
 - :cpp:func:`lammps_extract_setting`
 - :cpp:func:`lammps_extract_global_datatype`
 - :cpp:func:`lammps_extract_global`
+- :cpp:func:`lammps_extract_pair_dimension`
+- :cpp:func:`lammps_extract_pair`
 - :cpp:func:`lammps_map_atom`
 
 --------------------
@@ -123,6 +125,16 @@ subdomains and processors.
 
 -----------------------
 
+.. doxygenfunction:: lammps_extract_pair_dimension
+   :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_extract_pair
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_map_atom
    :project: progguide
 

doc/src/Packages_details.rst

@@ -8,12 +8,12 @@ info on how to download or build any extra library it requires.  It also
 gives links to documentation, example scripts, and pictures/movies (if
 available) that illustrate use of the package.
 
-The majority of packages can be included in a LAMMPS build with a
+The majority of packages can be included in a LAMMPS build with a single
-single setting (``-D PKG_<NAME>=on`` for CMake) or command
+setting (``-D PKG_<NAME>=on`` for CMake) or command (``make yes-<name>``
-(``make yes-<name>`` for make).  See the :doc:`Build package <Build_package>`
+for make).  See the :doc:`Build package <Build_package>` page for more
-page for more info.  A few packages may require additional steps;
+info.  A few packages may require additional steps; this is indicated in
-this is indicated in the descriptions below.  The :doc:`Build extras <Build_extras>`
+the descriptions below.  The :doc:`Build extras <Build_extras>` page
-page gives those details.
+gives those details.
 
 .. note::
 
@@ -103,6 +103,7 @@ page gives those details.
    * :ref:`QEQ <PKG-QEQ>`
    * :ref:`QMMM <PKG-QMMM>`
    * :ref:`QTB <PKG-QTB>`
+   * :ref:`RHEO <PKG-RHEO>`
    * :ref:`REACTION <PKG-REACTION>`
    * :ref:`REAXFF <PKG-REAXFF>`
    * :ref:`REPLICA <PKG-REPLICA>`
@@ -1323,18 +1324,19 @@ KSPACE package
 
 **Contents:**
 
-A variety of long-range Coulombic solvers, as well as pair styles
+A variety of long-range Coulombic solvers, as well as pair styles which
-which compute the corresponding short-range pairwise Coulombic
+compute the corresponding short-range pairwise Coulombic interactions.
-interactions.  These include Ewald, particle-particle particle-mesh
+These include Ewald, particle-particle particle-mesh (PPPM), and
-(PPPM), and multilevel summation method (MSM) solvers.
+multilevel summation method (MSM) solvers.
 
 **Install:**
 
-Building with this package requires a 1d FFT library be present on
+Building with this package requires a 1d FFT library be present on your
-your system for use by the PPPM solvers.  This can be the KISS FFT
+system for use by the PPPM solvers.  This can be the KISS FFT library
-library provided with LAMMPS, third party libraries like FFTW, or a
+provided with LAMMPS, third party libraries like FFTW, or a
-vendor-supplied FFT library.  See the :doc:`Build settings <Build_settings>` page for details on how to select
+vendor-supplied FFT library.  See the :doc:`Build settings
-different FFT options for your LAMPMS build.
+<Build_settings>` page for details on how to select different FFT
+options for your LAMMPS build.
 
 **Supporting info:**
 
@@ -2621,6 +2623,45 @@ another set.
 
 ----------
 
+.. _PKG-RHEO:
+
+RHEO package
+------------
+
+**Contents:**
+
+Pair styles, bond styles, fixes, and computes for reproducing
+hydrodynamics and elastic objects. See the :doc:`Howto rheo
+<Howto_rheo>` page for an overview.
+
+**Install:**
+
+This package has :ref:`specific installation instructions <rheo>` on the :doc:`Build extras <Build_extras>` page.
+
+**Authors:** Joel T. Clemmer (Sandia National Labs),
+Thomas C. O'Connor (Carnegie Mellon University)
+
+.. versionadded:: TBD
+
+**Supporting info:**
+
+* src/RHEO filenames -> commands
+* :doc:`Howto_rheo <Howto_rheo>`
+* :doc:`atom_style rheo <atom_style>`
+* :doc:`atom_style rheo/thermal <atom_style>`
+* :doc:`bond_style rheo/shell <bond_rheo_shell>`
+* :doc:`compute rheo/property/atom <compute_rheo_property_atom>`
+* :doc:`fix rheo <fix_rheo>`
+* :doc:`fix rheo/oxidation <fix_rheo_oxidation>`
+* :doc:`fix rheo/pressure <fix_rheo_pressure>`
+* :doc:`fix rheo/thermal <fix_rheo_thermal>`
+* :doc:`fix rheo/viscosity <fix_rheo_viscosity>`
+* :doc:`pair_style rheo <pair_rheo>`
+* :doc:`pair_style rheo/solid <pair_rheo_solid>`
+* examples/rheo
+
+----------
+
 .. _PKG-RIGID:
 
 RIGID package

doc/src/Packages_list.rst

@@ -413,6 +413,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>`
      - qtb
      - no
+   * - :ref:`RHEO <PKG-RHEO>`
+     - reproducing hydrodynamics and elastic objects
+     - :doc:`Howto rheo <Howto_rheo>`
+     - rheo
+     - no
    * - :ref:`REACTION <PKG-REACTION>`
      - chemical reactions in classical MD
      - :doc:`fix bond/react <fix_bond_react>`

doc/src/Tools.rst

@@ -92,7 +92,6 @@ Miscellaneous tools
    * :ref:`emacs <emacs>`
    * :ref:`i-PI <ipi>`
    * :ref:`kate <kate>`
-   * :ref:`LAMMPS shell <lammps_shell>`
    * :ref:`LAMMPS GUI <lammps_gui>`
    * :ref:`LAMMPS magic patterns for file(1) <magic>`
    * :ref:`Offline build tool <offline>`
@@ -379,7 +378,7 @@ See README file in the tools/fep directory.
 i-PI tool
 -------------------
 
-.. versionchanged:: TBD
+.. versionchanged:: 27June2024
 
 The tools/i-pi directory used to contain a bundled version of the i-PI
 software package for use with LAMMPS.  This version, however, was
@@ -389,7 +388,7 @@ The i-PI package was created and is maintained by Michele Ceriotti,
 michele.ceriotti at gmail.com, to interface to a variety of molecular
 dynamics codes.
 
-i-PI is now available via PyPi using the pip package manager at:
+i-PI is now available via PyPI using the pip package manager at:
 https://pypi.org/project/ipi/
 
 Here are the commands to set up a virtual environment and install
@@ -444,219 +443,9 @@ The file was provided by Alessandro Luigi Sellerio
 
 ----------
 
-.. _lammps_shell:
-
-LAMMPS shell
-------------
-
-.. versionadded:: 9Oct2020
-
-Overview
-^^^^^^^^
-
-The LAMMPS Shell, ``lammps-shell`` is a program that functions very
-similar to the regular LAMMPS executable but has several modifications
-and additions that make it more powerful for interactive sessions,
-i.e. where you type LAMMPS commands from the prompt instead of reading
-them from a file.
-
-- It uses the readline and history libraries to provide command line
-  editing and context aware TAB-expansion (details on that below).
-
-- When processing an input file with the '-in' or '-i' flag from the
-  command line, it does not exit at the end of that input file but
-  stops at a prompt, so that additional commands can be issued
-
-- Errors will not abort the shell but return to the prompt.
-
-- It has additional commands aimed at interactive use (details below).
-
-- Interrupting a calculation with CTRL-C will not terminate the
-  session but rather enforce a timeout to cleanly stop an ongoing
-  run (more info on timeouts is in the :doc:`timer command <timer>`
-  documentation).
-
-These enhancements make the LAMMPS shell an attractive choice for
-interactive LAMMPS sessions in graphical desktop environments
-(e.g. Gnome, KDE, Cinnamon, XFCE, Windows).
-
-TAB-expansion
-^^^^^^^^^^^^^
-
-When writing commands interactively at the shell prompt, you can hit
-the TAB key at any time to try and complete the text.  This completion
-is context aware and will expand any first word only to commands
-available in that executable.
-
-- For style commands it will expand to available styles of the
-  corresponding category (e.g. pair styles after a
-  :doc:`pair_style <pair_style>` command).
-
-- For :doc:`compute <compute>`, :doc:`fix <fix>`, or :doc:`dump <dump>`
-  it will also expand only to already defined groups for the group-ID
-  keyword.
-
-- For commands like :doc:`compute_modify <compute_modify>`,
-  :doc:`fix_modify <fix_modify>`, or :doc:`dump_modify <dump_modify>`
-  it will expand to known compute/fix/dump IDs only.
-
-- When typing references to computes, fixes, or variables with a
-  "c\_", "f\_", or "v\_" prefix, respectively, then the expansion will
-  be to known compute/fix IDs and variable names. Variable name
-  expansion is also available for the ${name} variable syntax.
-
-- In all other cases TAB expansion will complete to names of files
-  and directories.
-
-Command line editing and history
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-When typing commands, command line editing similar to what BASH
-provides is available.  Thus it is possible to move around the
-currently line and perform various cut and insert and edit operations.
-Previous commands can be retrieved by scrolling up (and down)
-or searching (e.g. with CTRL-r).
-
-Also history expansion through using the exclamation mark '!'
-can be performed.  Examples: '!!' will be replaced with the previous
-command, '!-2' will repeat the command before that, '!30' will be
-replaced with event number 30 in the command history list, and
-'!run' with the last command line that started with "run".  Adding
-a ":p" to such a history expansion will result that the expansion is
-printed and added to the history list, but NOT executed.
-On exit the LAMMPS shell will write the history list to a file
-".lammps_history" in the current working directory.  If such a
-file exists when the LAMMPS shell is launched it will be read to
-populate the history list.
-
-This is realized via the readline library and can thus be customized
-with an ``.inputrc`` file in the home directory.  For application
-specific customization, the LAMMPS shell uses the name "lammps-shell".
-For more information about using and customizing an application using
-readline, please see the available documentation at:
-https://www.gnu.org/software/readline/
-
-
-Additional commands
-^^^^^^^^^^^^^^^^^^^
-
-The following commands are added to the LAMMPS shell on top of the
-regular LAMMPS commands:
-
-.. parsed-literal::
-
-   help (or ?)    print a brief help message
-   history        display the current command history list
-   clear_history  wipe out the current command history list
-   save_history <range> <file>
-                  write commands from the history to file.
-                  The range is given as <from>-<to>, where <from> and <to>
-                  may be empty. Example: save_history 100- in.recent
-   source <file>  read commands from file (same as "include")
-   pwd            print current working directory
-   cd <directory> change current working directory (same as pwd if no directory)
-   mem            print current and maximum memory usage
-   \|<command>     execute <command> as a shell command and return to the command prompt
-   exit           exit the LAMMPS shell cleanly (unlike the "quit" command)
-
-Please note that some known shell operations are implemented in the
-LAMMPS :doc:`shell command <shell>` in a platform neutral fashion,
-while using the '\|' character will always pass the following text
-to the operating system's shell command.
-
-Compilation
-^^^^^^^^^^^
-
-Compilation of the LAMMPS shell can be enabled by setting the CMake
-variable ``BUILD_LAMMPS_SHELL`` to "on" or using the makefile in the
-``tools/lammps-shell`` folder to compile after building LAMMPS using
-the conventional make procedure.  The makefile will likely need
-customization depending on the features and settings used for
-compiling LAMMPS.
-
-Limitations
-^^^^^^^^^^^
-
-The LAMMPS shell was not designed for use with MPI parallelization
-via ``mpirun`` or ``mpiexec`` or ``srun``.
-
-Readline customization
-^^^^^^^^^^^^^^^^^^^^^^
-
-The behavior of the readline functionality can be customized in the
-``${HOME}/.inputrc`` file.  This can be used to alter the default
-settings or change the key-bindings.  The LAMMPS Shell sets the
-application name ``lammps-shell``, so settings can be either applied
-globally or only for the LAMMPS shell by bracketing them between
-``$if lammps-shell`` and ``$endif`` like in the following example:
-
-.. code-block:: bash
-
-   $if lammps-shell
-   # disable "beep" or "screen flash"
-   set bell-style none
-   # bind the "Insert" key to toggle overwrite mode
-   "\e[2~": overwrite-mode
-   $endif
-
-More details about this are in the `readline documentation <https://tiswww.cwru.edu/php/chet/readline/rluserman.html#SEC9>`_.
-
-
-LAMMPS Shell tips and tricks
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Below are some suggestions for how to use and customize the LAMMPS shell.
-
-Enable tilde expansion
-""""""""""""""""""""""
-
-Adding ``set expand-tilde on`` to ``${HOME}/.inputrc`` is recommended as
-this will change the filename expansion behavior to replace any text
-starting with "~" by the full path to the corresponding user's home
-directory.  While the expansion of filenames **will** happen on all
-arguments where the context is not known (e.g. ``~/compile/lamm<TAB>``
-will expand to ``~/compile/lammps/``), it will not replace the tilde by
-default.  But since LAMMPS does not do tilde expansion itself (unlike a
-shell), this will result in errors.  Instead the tilde-expression should
-be expanded into a valid path, where the plain "~/" stands for the
-current user's home directory and "~someuser/" stands for
-"/home/someuser" or whatever the full path to that user's home directory
-is.
-
-File extension association
-""""""""""""""""""""""""""
-
-Since the LAMMPS shell (unlike the regular LAMMPS executable) does not
-exit when an input file is passed on the command line with the "-in" or
-"-i" flag (the behavior is like for ``python -i <filename>``), it makes
-the LAMMPS shell suitable for associating it with input files based on
-their filename extension (e.g. ".lmp").  Since ``lammps-shell`` is a
-console application, you have to run it inside a terminal program with a
-command line like this:
-
-.. code-block:: bash
-
-   xterm -title "LAMMPS Shell" -e /path/to/lammps-shell -i in.file.lmp
-
-
-Use history to create an input file
-"""""""""""""""""""""""""""""""""""
-
-When experimenting with commands to interactively to figure out a
-suitable choice of settings or simply the correct syntax, you may want
-to record part of your commands to a file for later use.  This can be
-done with the ``save_history`` commands, which allows to selectively
-write a section of the command history to a file (Example:
-``save_history 25-30 in.run``).  This file can be further edited
-(Example: ``|vim in.run``) and then the file read back in and tried out
-(Example: ``source in.run``).  If the input also creates a system box,
-you first need to use the :doc:`clear` command.
-
-----------
-
 .. _lammps_gui:
 
-LAMMPS GUI
+LAMMPS-GUI
 ----------
 
 .. versionadded:: 2Aug2023
@@ -664,25 +453,28 @@ LAMMPS GUI
 Overview
 ^^^^^^^^
 
-LAMMPS GUI is a graphical text editor customized for editing LAMMPS
+LAMMPS-GUI is a graphical text editor customized for editing LAMMPS
 input files that is linked to the :ref:`LAMMPS C-library <lammps_c_api>`
 and thus can run LAMMPS directly using the contents of the editor's text
 buffer as input.  It can retrieve and display information from LAMMPS
 while it is running, display visualizations created with the :doc:`dump
 image command <dump_image>`, and is adapted specifically for editing
-LAMMPS input files through text completion and reformatting, and linking
+LAMMPS input files through syntax highlighting, text completion, and
-to the online LAMMPS documentation for known LAMMPS commands and styles.
+reformatting, and linking to the online LAMMPS documentation for known
+LAMMPS commands and styles.
 
-This is similar to what people traditionally would do to run LAMMPS:
+This is similar to what people traditionally would do to run LAMMPS but
-using a regular text editor to edit the input and run the necessary
+all rolled into a single application: that is, using a text editor,
-commands, possibly including the text editor, too, from a command line
+plotting program, and a visualization program to edit the input, run
-terminal window.  This similarity is a design goal. While making it easy
+LAMMPS, process the output into graphs and visualizations from a command
-for beginners to start with LAMMPS, it is also the intention to simplify
+line window.  This similarity is a design goal. While making it easy for
-the transition to workflows like most experienced LAMMPS users do.
+beginners to start with LAMMPS, it is also the expectation that
+LAMMPS-GUI users will eventually transition to workflows that most
+experienced LAMMPS users employ.
 
 All features have been extensively exposed to keyboard shortcuts, so
 that there is also appeal for experienced LAMMPS users for prototyping
-and testing simulations setups.
+and testing simulation setups.
 
 Features
 ^^^^^^^^
@@ -690,9 +482,10 @@ Features
 A detailed discussion and explanation of all features and functionality
 are in the :doc:`Howto_lammps_gui` tutorial Howto page.
 
-Here are a few highlights of LAMMPS GUI
+Here are a few highlights of LAMMPS-GUI
 
 - Text editor with syntax highlighting customized for LAMMPS
+- Text editor features command completion for known commands and styles
 - Text editor will switch working directory to folder of file in buffer
 - Text editor will remember up to 5 recent files
 - Context specific LAMMPS command help via online documentation
@@ -704,32 +497,32 @@ Here are a few highlights of LAMMPS GUI
 - Thermodynamic output is captured and displayed as line graph in a Chart Window
 - Indicator for currently executed command
 - Indicator for line that caused an error
-- Visualization of current state in Image Viewer (via :doc:`dump image <dump_image>`)
+- Visualization of current state in Image Viewer (via calling :doc:`write_dump image <dump_image>`)
+- Capture of images created via :doc:`dump image <dump_image>` in Slide show window
 - Many adjustable settings and preferences that are persistent
-- Dialog to set variables from the LAMMPS command line
+- Dialog to set variables, similar to the LAMMPS command line flag '-v' / '-var'
 
 Parallelization
 ^^^^^^^^^^^^^^^
 
 Due to its nature as a graphical application, it is not possible to use
-the LAMMPS GUI in parallel with MPI, but OpenMP multi-threading and GPU
+the LAMMPS-GUI in parallel with MPI, but OpenMP multi-threading and GPU
 acceleration is available and enabled by default.
 
 Prerequisites and portability
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-LAMMPS GUI is programmed in C++ based on the C++11 standard and using
+LAMMPS-GUI is programmed in C++ based on the C++11 standard and using
 the `Qt GUI framework <https://www.qt.io/product/framework>`_.
 Currently, Qt version 5.12 or later is required; Qt 5.15LTS is
-recommended; support for Qt version 6.x is under active development and
+recommended; support for Qt version 6.x is available.  Building LAMMPS
-thus far only tested with Qt 6.5LTS on Linux.  Building LAMMPS with
+with CMake is required.
-CMake is required.
 
-The LAMMPS GUI has been successfully compiled and tested on:
+The LAMMPS-GUI has been successfully compiled and tested on:
 
 - Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
 - Fedora Linux 40 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS
-- Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.5LTS
+- Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.7
 - Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
 - Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
 - Windows 10 and 11 x86_64 with MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS
@@ -745,20 +538,20 @@ available from https://download.lammps.org/static or
 https://github.com/lammps/lammps/releases.  You can unpack the archives
 (or mount the macOS disk image) and run the GUI directly in place. The
 folder may also be moved around and added to the ``PATH`` environment
-variable so the executables will be found automatically.  The LAMMPS GUI
+variable so the executables will be found automatically.  The LAMMPS-GUI
 executable is called ``lammps-gui`` and either takes no arguments or
 attempts to load the first argument as LAMMPS input file.
 
 Compilation
 ^^^^^^^^^^^
 
-The source for the LAMMPS GUI is included with the LAMMPS source code
+The source for the LAMMPS-GUI is included with the LAMMPS source code
 distribution in the folder ``tools/lammps-gui`` and thus it can be can
 be built as part of a regular LAMMPS compilation.  :doc:`Using CMake
 <Howto_cmake>` is required.  To enable its compilation, the CMake
 variable ``-D BUILD_LAMMPS_GUI=on`` must be set when creating the CMake
 configuration.  All other settings (compiler, flags, compile type) for
-LAMMPS GUI are then inherited from the regular LAMMPS build.  If the Qt
+LAMMPS-GUI are then inherited from the regular LAMMPS build.  If the Qt
 library is packaged for Linux distributions, then its location is
 typically auto-detected since the required CMake configuration files are
 stored in a location where CMake can find them without additional help.
@@ -766,17 +559,17 @@ Otherwise, the location of the Qt library installation must be indicated
 by setting ``-D Qt5_DIR=/path/to/qt5/lib/cmake/Qt5``, which is a path to
 a folder inside the Qt installation that contains the file
 ``Qt5Config.cmake``. Similarly, for Qt6 the location of the Qt library
-installation can be indicated by setting ``-D Qt6_DIR=/path/to/qt6/lib/cmake/Qt6``,
+installation can be indicated by setting ``-D
-if necessary.  When both, Qt5 and Qt6 are available, Qt6 will be preferred
+Qt6_DIR=/path/to/qt6/lib/cmake/Qt6``, if necessary.  When both, Qt5 and
-unless ``-D LAMMPS_GUI_USE_QT5=yes`` is set.
+Qt6 are available, Qt6 will be preferred unless ``-D
+LAMMPS_GUI_USE_QT5=yes`` is set.
 
-It should be possible to build the LAMMPS GUI as a standalone
+It is possible to build the LAMMPS-GUI as a standalone compilation
-compilation (e.g. when LAMMPS has been compiled with traditional make).
+(e.g. when LAMMPS has been compiled with traditional make).  Then the
-Then the CMake configuration needs to be told where to find the LAMMPS
+CMake configuration needs to be told where to find the LAMMPS headers
-headers and the LAMMPS library, via ``-D
+and the LAMMPS library, via ``-D LAMMPS_SOURCE_DIR=/path/to/lammps/src``.
-LAMMPS_SOURCE_DIR=/path/to/lammps/src``.  CMake will try to guess a
+CMake will try to guess a build folder with the LAMMPS library from that
-build folder with the LAMMPS library from that path, but it can also be
+path, but it can also be set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``.
-set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``.
 
 Rather than linking to the LAMMPS library during compilation, it is also
 possible to compile the GUI with a plugin loader that will load
@@ -827,19 +620,19 @@ There is a custom `x64-GUI-MSVC` build configuration provided in the
 compilation settings for project.  Choosing this configuration will
 activate building the `lammps-gui.exe` executable in addition to LAMMPS
 through importing package selection from the ``windows.cmake`` preset
-file and enabling building the LAMMPS GUI and disabling building with MPI.
+file and enabling building the LAMMPS-GUI and disabling building with MPI.
 When requesting an installation from the `Build` menu in Visual Studio,
 it will create a compressed ``LAMMPS-Win10-amd64.zip`` zip file with the
 executables and required dependent .dll files.  This zip file can be
 uncompressed and ``lammps-gui.exe`` run directly from there.  The
 uncompressed folder can be added to the ``PATH`` environment and LAMMPS
-and LAMMPS GUI can be launched from anywhere from the command line.
+and LAMMPS-GUI can be launched from anywhere from the command line.
 
 **MinGW64 Cross-compiler**
 
 The standard CMake build procedure can be applied and the
 ``mingw-cross.cmake`` preset used. By using ``mingw64-cmake`` the CMake
-command will automatically include a suitable CMake toolset file (the
+command will automatically include a suitable CMake toolchain file (the
 regular cmake command can be used after that to modify the configuration
 settings, if needed).  After building the libraries and executables,
 you can build the target 'zip' (i.e. ``cmake --build <build dir> --target zip``
@@ -1329,7 +1122,7 @@ for Tcl with:
 .. code-block:: bash
 
    swig -tcl -module tcllammps lammps.i
-   gcc -fPIC -shared $(pkgconf --cflags tcl) -o tcllammps.so \
+   gcc -fPIC -shared $(pkg-config tcl --cflags) -o tcllammps.so \
                lammps_wrap.c -L ../src/ -llammps
    tclsh
 
@@ -1340,8 +1133,8 @@ functions included with:
 
    swig -tcl -module tcllmps lammps_shell.i
    gcc -o tcllmpsh lammps_wrap.c -Xlinker -export-dynamic \
-            -DHAVE_CONFIG_H $(pkgconf --cflags tcl) \
+            -DHAVE_CONFIG_H $(pkg-config tcl --cflags) \
-            $(pkgconf --libs tcl) -L ../src -llammps
+            $(pkg-config tcl --libs) -L ../src -llammps
 
 In both cases it is assumed that the LAMMPS library was compiled
 as a shared library in the ``src`` folder. Otherwise the last

doc/src/atom_modify.rst

@@ -71,11 +71,11 @@ all atoms, e.g. in a data or restart file.
    atom IDs are required, due to how neighbor lists are built.
 
 The *map* keyword determines how atoms with specific IDs are found
-when required.  An example are the bond (angle, etc) methods which
+when required.  For example, the bond (angle, etc) methods need to
-need to find the local index of an atom with a specific global ID
+find the local index of an atom with a specific global ID which is a
-which is a bond (angle, etc) partner.  LAMMPS performs this operation
+bond (angle, etc) partner.  LAMMPS performs this operation efficiently
-efficiently by creating a "map", which is either an *array* or *hash*
+by creating a "map", which is either an *array* or *hash* table, as
-table, as described below.
+described below.
 
 When the *map* keyword is not specified in your input script, LAMMPS
 only creates a map for :doc:`atom_styles <atom_style>` for molecular
@@ -83,34 +83,39 @@ systems which have permanent bonds (angles, etc).  No map is created
 for atomic systems, since it is normally not needed.  However some
 LAMMPS commands require a map, even for atomic systems, and will
 generate an error if one does not exist.  The *map* keyword thus
-allows you to force the creation of a map.  The *yes* value will
+allows you to force the creation of a map.
-create either an *array* or *hash* style map, as explained in the next
-paragraph.  The *array* and *hash* values create an array-style or
-hash-style map respectively.
 
-For an *array*\ -style map, each processor stores a lookup table of
+Specifying a value of *yes* will create either an array-style or
-length N, where N is the largest atom ID in the system.  This is a
+hash-style map, depending on the size of the system.  If no atom ID is
-fast, simple method for many simulations, but requires too much memory
+larger than 1 million, then an array-style map is used, otherwise a
-for large simulations.  For a *hash*\ -style map, a hash table is
+hash-style map is used.  Specifying a value of *array* or *hash*
-created on each processor, which finds an atom ID in constant time
+creates an array-style or hash-style map respectively, regardless of
-(independent of the global number of atom IDs).  It can be slightly
+the size of the system.
-slower than the *array* map, but its memory cost is proportional to
-the number of atoms owned by a processor, i.e. N/P when N is the total
-number of atoms in the system and P is the number of processors.
 
-The *first* keyword allows a :doc:`group <group>` to be specified whose
+For an array-style map, each processor stores a lookup table of length
-atoms will be maintained as the first atoms in each processor's list
+N, where N is the largest atom ID in the system.  This is a fast,
-of owned atoms.  This in only useful when the specified group is a
+simple method for many simulations, but requires too much memory for
-small fraction of all the atoms, and there are other operations LAMMPS
+large simulations.  For a hash-style map, a hash table is created on
-is performing that will be sped-up significantly by being able to loop
+each processor, which finds an atom ID in constant time (independent
-over the smaller set of atoms.  Otherwise the reordering required by
+of the global number of atom IDs).  It can be slightly slower than the
-this option will be a net slow-down.  The :doc:`neigh_modify include <neigh_modify>` and :doc:`comm_modify group <comm_modify>`
+*array* map, but its memory cost is proportional to the number of
-commands are two examples of commands that require this setting to
+atoms owned by a processor, i.e. N/P when N is the total number of
-work efficiently.  Several :doc:`fixes <fix>`, most notably time
+atoms in the system and P is the number of processors.
-integration fixes like :doc:`fix nve <fix_nve>`, also take advantage of
+
-this setting if the group they operate on is the group specified by
+The *first* keyword allows a :doc:`group <group>` to be specified
-this command.  Note that specifying "all" as the group-ID effectively
+whose atoms will be maintained as the first atoms in each processor's
-turns off the *first* option.
+list of owned atoms.  This in only useful when the specified group is
+a small fraction of all the atoms, and there are other operations
+LAMMPS is performing that will be sped-up significantly by being able
+to loop over the smaller set of atoms.  Otherwise the reordering
+required by this option will be a net slow-down.  The
+:doc:`neigh_modify include <neigh_modify>` and :doc:`comm_modify group
+<comm_modify>` commands are two examples of commands that require this
+setting to work efficiently.  Several :doc:`fixes <fix>`, most notably
+time integration fixes like :doc:`fix nve <fix_nve>`, also take
+advantage of this setting if the group they operate on is the group
+specified by this command.  Note that specifying "all" as the group-ID
+effectively turns off the *first* option.
 
 It is OK to use the *first* keyword with a group that has not yet been
 defined, e.g. to use the atom_modify first command at the beginning of
@@ -148,15 +153,16 @@ cache locality will be undermined.
 
 .. note::
 
-   Running a simulation with sorting on versus off should not
+   Running a simulation with sorting on versus off should not change
-   change the simulation results in a statistical sense.  However, a
+   the simulation results in a statistical sense.  However, a
-   different ordering will induce round-off differences, which will lead
+   different ordering will induce round-off differences, which will
-   to diverging trajectories over time when comparing two simulations.
+   lead to diverging trajectories over time when comparing two
-   Various commands, particularly those which use random numbers
+   simulations.  Various commands, particularly those which use random
-   (e.g. :doc:`velocity create <velocity>`, and :doc:`fix langevin <fix_langevin>`), may generate (statistically identical)
+   numbers (e.g. :doc:`velocity create <velocity>`, and :doc:`fix
-   results which depend on the order in which atoms are processed.  The
+   langevin <fix_langevin>`), may generate (statistically identical)
-   order of atoms in a :doc:`dump <dump>` file will also typically change
+   results which depend on the order in which atoms are processed.
-   if sorting is enabled.
+   The order of atoms in a :doc:`dump <dump>` file will also typically
+   change if sorting is enabled.
 
 .. note::
 
@@ -183,12 +189,13 @@ Default
 
 By default, *id* is yes.  By default, atomic systems (no bond topology
 info) do not use a map.  For molecular systems (with bond topology
-info), a map is used.  The default map style is array if no atom ID is
+info), the default is to use a map of either *array* or *hash* style
-larger than 1 million, otherwise the default is hash.  By default, a
+depending on the size of the system, as explained above for the *map
-"first" group is not defined.  By default, sorting is enabled with a
+yes* keyword/value option.  By default, a *first* group is not
-frequency of 1000 and a binsize of 0.0, which means the neighbor
+defined.  By default, sorting is enabled with a frequency of 1000 and
-cutoff will be used to set the bin size. If no neighbor cutoff is
+a binsize of 0.0, which means the neighbor cutoff will be used to set
-defined, sorting will be turned off.
+the bin size. If no neighbor cutoff is defined, sorting will be turned
+off.
 
 ----------
 

doc/src/atom_style.rst

@@ -189,6 +189,14 @@ the Additional Information section below.
      - *atomic* + molecule, radius, rmass + "smd data"
      - :ref:`MACHDYN <PKG-MACHDYN>`
      - Smooth Mach Dynamics models
+   * - *rheo*
+     - *atomic* + rho, status
+     - :ref:`RHEO <PKG-RHEO>`
+     - solid and fluid RHEO particles
+   * - *rheo/thermal*
+     - *atomic* + rho, status, energy, temperature
+     - :ref:`RHEO <PKG-RHEO>`
+     - RHEO particles with temperature
    * - *sph*
      - *atomic* + "sph data"
      - :ref:`SPH <PKG-SPH>`

doc/src/bond_rheo_shell.rst

@@ -0,0 +1,188 @@
+.. index:: bond_style rheo/shell
+
+bond_style rheo/shell command
+=============================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   bond_style rheo/shell keyword value attribute1 attribute2 ...
+
+* required keyword = *t/form*
+* optional keyword = *store/local*
+
+  .. parsed-literal::
+
+       *t/form* value = formation time for a bond (time units)
+
+       *store/local* values = fix_ID N attributes ...
+          * fix_ID = ID of associated internal fix to store data
+          * N = prepare data for output every this many timesteps
+          * attributes = zero or more of the below attributes may be appended
+
+            *id1, id2* = IDs of 2 atoms in the bond
+            *time* = the timestep the bond broke
+            *x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units)
+            *x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   bond_style rheo/shell t/form 10.0
+   bond_coeff 1 1.0 0.05 0.1
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+The *rheo/shell* bond style is designed to work with
+:doc:`fix rheo/oxidation <fix_rheo_oxidation>` which creates candidate
+bonds between eligible surface or near-surface particles. When a bond
+is first created, it computes no forces and starts a timer. Forces are
+not computed until the timer reaches the specified bond formation time,
+*t/form*, and the bond is enabled and applies forces. If the two particles
+move outside of the maximum bond distance or move into the bulk before
+the timer reaches *t/form*, the bond automatically deletes itself. This
+deletion is not recorded as a broken bond in the optional *store/local* fix.
+
+Before bonds are enabled, they are still treated as regular bonds by
+all other parts of LAMMPS. This means they are written to data files
+and counted in computes such as :doc:`nbond/atom <compute_nbond_atom>`.
+To only count enabled bonds, use the *nbond/shell* attribute in
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`.
+
+When enabled, the bond then computes forces based on deviations from
+the initial reference state of the two atoms much like a BPM style
+bond (as further discussed in the :doc:`BPM howto page <Howto_bpm>`).
+The reference state is stored by each bond when it is first enabled.
+Data is then preserved across run commands and is written to
+:doc:`binary restart files <restart>` such that restarting the system
+will not reset the reference state of a bond or the timer.
+
+This bond style is based on a model described in
+:ref:`(Clemmer) <rheo_clemmer>`. The force has a magnitude of
+
+.. math::
+
+   F = 2 k (r - r_0) + \frac{2 k}{r_0^2 \epsilon_c^2} (r - r_0)^3
+
+where :math:`k` is a stiffness, :math:`r` is the current distance
+and :math:`r_0` is the initial distance between the two particles, and
+:math:`\epsilon_c` is maximum strain beyond which a bond breaks. This
+is done by setting the bond type to 0 such that forces are no longer
+computed.
+
+A damping force proportional to the difference in the normal velocity
+of particles is also applied to bonded particles:
+
+.. math::
+
+   F_D = - \gamma w (\hat{r} \bullet \vec{v})
+
+where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
+displacement normal vector, and :math:`\vec{v}` is the velocity difference
+between the two particles.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read_data
+<read_data>` or :doc:`read_restart <read_restart>` commands:
+
+* :math:`k`             (force/distance units)
+* :math:`\epsilon_c`    (unit less)
+* :math:`\gamma`        (force/velocity units)
+
+Unlike other BPM-style bonds, this bond style does not update special
+bond settings when bonds are created or deleted. This bond style also
+does not enforce specific :doc:`special_bonds <special_bonds>` settings.
+This behavior is purposeful such :doc:`RHEO pair <pair_rheo>` forces
+and heat flows are still calculated.
+
+If the *store/local* keyword is used, an internal fix will track bonds that
+break during the simulation. Whenever a bond breaks, data is processed
+and transferred to an internal fix labeled *fix_ID*. This allows the
+local data to be accessed by other LAMMPS commands. Following this optional
+keyword, a list of one or more attributes is specified.  These include the
+IDs of the two atoms in the bond. The other attributes for the two atoms
+include the timestep during which the bond broke and the current/initial
+center of mass position of the two atoms.
+
+Data is continuously accumulated over intervals of *N*
+timesteps. At the end of each interval, all of the saved accumulated
+data is deleted to make room for new data. Individual datum may
+therefore persist anywhere between *1* to *N* timesteps depending on
+when they are saved. This data can be accessed using the *fix_ID* and a
+:doc:`dump local <dump>` command. To ensure all data is output,
+the dump frequency should correspond to the same interval of *N*
+timesteps. A dump frequency of an integer multiple of *N* can be used
+to regularly output a sample of the accumulated data.
+
+Note that when unbroken bonds are dumped to a file via the
+:doc:`dump local <dump>` command, bonds with type 0 (broken bonds)
+are not included.
+The :doc:`delete_bonds <delete_bonds>` command can also be used to
+query the status of broken bonds or permanently delete them, e.g.:
+
+.. code-block:: LAMMPS
+
+   delete_bonds all stats
+   delete_bonds all bond 0 remove
+
+----------
+
+Restart and other info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This bond style writes the reference state of each bond to
+:doc:`binary restart files <restart>`. Loading a restart
+file will properly restore bonds. However, the reference state is NOT
+written to data files. Therefore reading a data file will not
+restore bonds and will cause their reference states to be redefined.
+
+If the *store/local* option is used, an internal fix will calculate
+a local vector or local array depending on the number of input values.
+The length of the vector or number of rows in the array is the number
+of recorded, broken bonds.  If a single input is specified, a local
+vector is produced. If two or more inputs are specified, a local array
+is produced where the number of columns = the number of inputs.  The
+vector or array can be accessed by any command that uses local values
+from a compute as input. See the :doc:`Howto output <Howto_output>` page
+for an overview of LAMMPS output options.
+
+The vector or array will be floating point values that correspond to
+the specified attribute.
+
+The single() function of this bond style returns 0.0 for the energy
+of a bonded interaction, since energy is not conserved in these
+dissipative potentials.  The single() function also calculates two
+extra bond quantities, the initial distance :math:`r_0` and a time.
+These extra quantities can be accessed by the
+:doc:`compute bond/local <compute_bond_local>` command as *b1* and *b2*\ .
+
+Restrictions
+""""""""""""
+
+This bond style is part of the RHEO 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:`bond_coeff <bond_coeff>`, :doc:`fix rheo/oxidation <fix_rheo_oxidation>`
+
+Default
+"""""""
+
+NA
+
+----------
+
+.. _rheo_clemmer:
+
+**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

doc/src/bond_style.rst

@@ -105,6 +105,7 @@ accelerated styles exist.
 * :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
 * :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
 * :doc:`quartic <bond_quartic>` - breakable quartic bond
+* :doc:`rheo/shell <bond_rheo_shell>` - shell bond for oxidation modeling in RHEO
 * :doc:`special <bond_special>` - enable special bond exclusions for 1-5 pairs and beyond
 * :doc:`table <bond_table>` - tabulated by bond length
 

doc/src/compute.rst

@@ -272,6 +272,10 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`pe/mol/tally <compute_tally>` - potential energy between two groups of atoms separated into intermolecular and intramolecular components via the tally callback mechanism
 * :doc:`pe/tally <compute_tally>` - potential energy between two groups of atoms via the tally callback mechanism
 * :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
+* :doc:`pod/atom <compute_pod_atom>` - POD descriptors for each atom
+* :doc:`podd/atom <compute_pod_atom>` - derivative of POD descriptors for each atom
+* :doc:`pod/local <compute_pod_atom>` - local POD descriptors and their derivatives
+* :doc:`pod/global <compute_pod_atom>` - global POD descriptors and their derivatives
 * :doc:`pressure <compute_pressure>` - total pressure and pressure tensor
 * :doc:`pressure/alchemy <compute_pressure_alchemy>` - mixed system total pressure and pressure tensor for :doc:`fix alchemy <fix_alchemy>` runs
 * :doc:`pressure/uef <compute_pressure_uef>` - pressure tensor in the reference frame of an applied flow field
@@ -286,6 +290,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
 * :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
 * :doc:`reduce/region <compute_reduce>` - same as compute reduce, within a region
+* :doc:`rheo/property/atom <compute_rheo_property_atom>` - convert atom attributes in RHEO package to per-atom vectors/arrays
 * :doc:`rigid/local <compute_rigid_local>` - extract rigid body attributes
 * :doc:`saed <compute_saed>` - electron diffraction intensity on a mesh of reciprocal lattice nodes
 * :doc:`slcsa/atom <compute_slcsa_atom>` - perform Supervised Learning Crystal Structure Analysis (SL-CSA)

doc/src/compute_nbond_atom.rst

@@ -8,10 +8,17 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   compute ID group-ID nbond/atom
+   compute ID group-ID nbond/atom keyword value
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * nbond/atom = style name of this compute command
+* zero or more keyword/value pairs may be appended
+* keyword = *bond/type*
+
+  .. parsed-literal::
+
+       *bond/type* value = *btype*
+         *btype* = bond type included in count
 
 Examples
 """"""""
@@ -19,6 +26,7 @@ Examples
 .. code-block:: LAMMPS
 
    compute 1 all nbond/atom
+   compute 1 all nbond/atom bond/type 2
 
 Description
 """""""""""
@@ -31,6 +39,9 @@ the :doc:`Howto broken bonds <Howto_bpm>` page for more information.
 The number of bonds will be zero for atoms not in the specified
 compute group. This compute does not depend on Newton bond settings.
 
+If the keyword *bond/type* is specified, only bonds of *btype* are
+counted.
+
 Output info
 """""""""""
 

doc/src/compute_pod_atom.rst

@@ -0,0 +1,145 @@
+.. index:: compute pod/atom
+.. index:: compute podd/atom
+.. index:: compute pod/local
+.. index:: compute pod/global
+
+compute pod/atom command
+========================
+
+compute podd/atom command
+=========================
+
+compute pod/local command
+=========================
+
+compute pod/global command
+==========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   compute ID group-ID pod/atom param.pod coefficients.pod
+   compute ID group-ID podd/atom param.pod coefficients.pod
+   compute ID group-ID pod/local param.pod coefficients.pod
+   compute ID group-ID pod/global param.pod coefficients.pod
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* pod/atom = style name of this compute command
+* param.pod = the parameter file specifies parameters of the POD descriptors
+* coefficients.pod = the coefficient file specifies coefficients of the POD potential
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute d all pod/atom Ta_param.pod
+   compute dd all podd/atom Ta_param.pod
+   compute ldd all pod/local Ta_param.pod
+   compute gdd all podd/global Ta_param.pod
+   compute d all pod/atom Ta_param.pod Ta_coefficients.pod
+   compute dd all podd/atom Ta_param.pod Ta_coefficients.pod
+   compute ldd all pod/local Ta_param.pod Ta_coefficients.pod
+   compute gdd all podd/global Ta_param.pod Ta_coefficients.pod
+
+Description
+"""""""""""
+
+.. versionadded:: 27June2024
+
+Define a computation that calculates a set of quantities related to the
+POD descriptors of the atoms in a group. These computes are used
+primarily for calculating the dependence of energy and force components
+on the linear coefficients in the :doc:`pod pair_style <pair_pod>`,
+which is useful when training a POD potential to match target data. POD
+descriptors of an atom are characterized by the radial and angular
+distribution of neighbor atoms. The detailed mathematical definition is
+given in the papers by :ref:`(Nguyen and Rohskopf) <Nguyen20222c>`,
+:ref:`(Nguyen2023) <Nguyen20232c>`, :ref:`(Nguyen2024) <Nguyen20242c>`,
+and :ref:`(Nguyen and Sema) <Nguyen20243c>`.
+
+Compute *pod/atom* calculates the per-atom POD descriptors.
+
+Compute *podd/atom* calculates derivatives of the per-atom POD
+descriptors with respect to atom positions.
+
+Compute *pod/local* calculates the per-atom POD descriptors and their
+derivatives with respect to atom positions.
+
+Compute *pod/global* calculates the global POD descriptors and their
+derivatives with respect to atom positions.
+
+Examples how to use Compute POD commands are found in the directory
+``examples/PACKAGES/pod``.
+
+
+.. warning::
+
+   All of these compute styles produce *very* large per-atom output
+   arrays that scale with the total number of atoms in the system.
+   This will result in *very* large memory consumption for systems
+   with a large number of atoms.
+
+----------
+
+Output info
+"""""""""""
+
+Compute *pod/atom* produces an 2D array of size :math:`N \times M`,
+where :math:`N` is the number of atoms and :math:`M` is the number of
+descriptors. Each column corresponds to a particular POD descriptor.
+
+Compute *podd/atom* produces an 2D array of size :math:`N \times (M * 3
+N)`. Each column corresponds to a particular derivative of a POD
+descriptor.
+
+Compute *pod/local* produces an 2D array of size :math:`(1 + 3N) \times
+(M * N)`.  The first row contains the per-atom descriptors, and the last
+3N rows contain the derivatives of the per-atom descriptors with respect
+to atom positions.
+
+Compute *pod/global* produces an 2D array of size :math:`(1 + 3N) \times
+(M)`.  The first row contains the global descriptors, and the last 3N
+rows contain the derivatives of the global descriptors with respect to
+atom positions.
+
+Restrictions
+""""""""""""
+
+These computes are part of the ML-POD package.  They are only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fitpod <fitpod_command>`,
+:doc:`pair_style pod <pair_pod>`
+
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Nguyen20222c:
+
+**(Nguyen and Rohskopf)** Nguyen and Rohskopf,  Journal of Computational Physics, 480, 112030, (2023).
+
+.. _Nguyen20232c:
+
+**(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023).
+
+.. _Nguyen20242c:
+
+**(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024).
+
+.. _Nguyen20243c:
+
+**(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
+
+

doc/src/compute_rheo_property_atom.rst

@@ -0,0 +1,143 @@
+.. index:: compute rheo/property/atom
+
+compute rheo/property/atom command
+==================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   compute ID group-ID rheo/property/atom input1 input2 ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* rheo/property/atom = style name of this compute command
+* input = one or more atom attributes
+
+  .. parsed-literal::
+
+       possible attributes = phase, surface, surface/r,
+                             surface/divr, surface/n/a, coordination,
+                             shift/v/a, energy, temperature, heatflow,
+                             conductivity, cv, viscosity, pressure, rho,
+                             grad/v/ab, stress/v/ab, stress/t/ab, nbond/shell
+
+  .. parsed-literal::
+
+           *phase* = atom phase state
+           *surface* = atom surface status
+           *surface/r* = atom distance from the surface
+           *surface/divr* = divergence of position at atom position
+           *surface/n/a* = a-component of surface normal vector
+           *coordination* = coordination number
+           *shift/v/a* = a-component of atom shifting velocity
+           *energy* = atom energy
+           *temperature* = atom temperature
+           *heatflow* = atom heat flow
+           *conductivity* = atom conductivity
+           *cv* = atom specific heat
+           *viscosity* = atom viscosity
+           *pressure* = atom pressure
+           *rho* = atom density
+           *grad/v/ab* = ab-component of atom velocity gradient tensor
+           *stress/v/ab* = ab-component of atom viscous stress tensor
+           *stress/t/ab* = ab-component of atom total stress tensor (pressure and viscous)
+           *nbond/shell* = number of oxide bonds
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute 1 all rheo/property/atom phase surface/r surface/n/* pressure
+   compute 2 all rheo/property/atom shift/v/x grad/v/xx stress/v/*
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Define a computation that stores atom attributes specific to the RHEO
+package for each atom in the group.  This is useful so that the values
+can be used by other :doc:`output commands <Howto_output>` that take
+computes as inputs. See for example, the
+:doc:`compute reduce <compute_reduce>`,
+:doc:`fix ave/atom <fix_ave_atom>`,
+:doc:`fix ave/histo <fix_ave_histo>`,
+:doc:`fix ave/chunk <fix_ave_chunk>`, and
+:doc:`atom-style variable <variable>` commands.
+
+For vector attributes, e.g. *shift/v/*:math:`\alpha`, one must specify
+:math:`\alpha` as the *x*, *y*, or *z* component, e.g. *shift/v/x*.
+Alternatively, a wild card \* will include all components, *x* and *y* in
+2D or *x*, *y*, and *z* in 3D.
+
+For tensor attributes, e.g. *grad/v/*:math:`\alpha \beta`, one must specify
+both :math:`\alpha` and :math:`\beta` as  *x*, *y*, or *z*, e.g. *grad/v/xy*.
+Alternatively, a wild card \* will include all components. In 2D, this
+includes *xx*, *xy*, *yx*, and *yy*. In 3D, this includes *xx*, *xy*, *xz*,
+*yx*, *yy*, *yz*, *zx*, *zy*, and *zz*.
+
+Many properties require their respective fixes, listed below in related
+commands, be defined. For instance, the *viscosity* attribute is the
+viscosity of a particle calculated by
+:doc:`fix rheo/viscous <fix_rheo_viscosity>`. The meaning of less obvious
+properties is described below.
+
+The *phase* property indicates whether the particle is in a fluid state,
+a value of 0, or a solid state, a value of 1.
+
+The *surface* property indicates the surface designation produced by
+the *interface/reconstruct* option of :doc:`fix rheo <fix_rheo>`. Bulk
+particles have a value of 0, surface particles have a value of 1, and
+splash particles have a value of 2. The *surface/r* property is the
+distance from the surface, up to the kernel cutoff length. Surface particles
+have a value of 0. The *surface/n/*:math:`\alpha` properties are the
+components of the surface normal vector.
+
+The *shift/v/*:math:`\alpha` properties are the components of the shifting
+velocity produced by the *shift* option of :doc:`fix rheo <fix_rheo>`.
+
+The *nbond/shell* property is the number of shell bonds that have been
+activated from :doc:`bond style rheo/shell <bond_rheo_shell>`.
+
+The values are stored in a per-atom vector or array as discussed
+below.  Zeroes are stored for atoms not in the specified group or for
+quantities that are not defined for a particular particle in the group
+
+Output info
+"""""""""""
+
+This compute calculates a per-atom vector or per-atom array depending
+on the number of input values.  Generally, if a single input is specified,
+a per-atom vector is produced.  If two or more inputs are specified, a
+per-atom array is produced where the number of columns = the number of
+inputs. However, if a wild card \* is used for a vector or tensor, then
+the number of inputs is considered to be incremented by the dimension or
+the dimension squared, respectively. The vector or array can be accessed
+by any command that uses per-atom values from a compute as input.  See the
+:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+options.
+
+The vector or array values will be in whatever :doc:`units <units>` the
+corresponding attribute is in (e.g., density units for *rho*).
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dump custom <dump>`, :doc:`compute reduce <compute_reduce>`,
+:doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
+:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
+:doc:`fix rheo/pressure <fix_rheo_pressure>`,
+:doc:`fix rheo/thermal <fix_rheo_thermal>`,
+:doc:`fix rheo/oxdiation <fix_rheo_oxidation>`,
+:doc:`fix rheo <fix_rheo>`
+
+Default
+"""""""
+
+none

doc/src/dump_modify.rst

@@ -107,6 +107,13 @@ Syntax
 
        *checksum* args = *yes* or *no* (add checksum at end of zst file)
 
+* these keywords apply only to the vtk* dump style
+* keyword = *binary*
+
+  .. parsed-literal::
+
+       *binary* args = *yes* or *no* (select between binary and text mode VTK files)
+
 Examples
 """"""""
 
@@ -907,11 +914,11 @@ box size stored with the snapshot.
 
 ----------
 
-The COMPRESS package offers both GZ and Zstd compression variants of
+The :ref:`COMPRESS package <PKG-COMPRESS>` offers both GZ and Zstd
-styles atom, custom, local, cfg, and xyz. When using these styles the
+compression variants of styles atom, custom, local, cfg, and xyz. When
-compression level can be controlled by the :code:`compression_level`
+using these styles the compression level can be controlled by the
-keyword. File names with these styles have to end in either
+:code:`compression_level` keyword. File names with these styles have to
-:code:`.gz` or :code:`.zst`.
+end in either :code:`.gz` or :code:`.zst`.
 
 GZ supports compression levels from :math:`-1` (default), 0 (no compression),
 and 1 to 9, 9 being the best compression. The COMPRESS :code:`/gz` styles use 9
@@ -930,6 +937,17 @@ default and it can be disabled with the :code:`checksum` keyword.
 
 ----------
 
+The :ref:`VTK package <PKG-VTK>` offers writing dump files in `VTK file
+formats <https://www.vtk.org/>`_ that can be read by a variety of
+visualization tools based on the VTK library.  These VTK files follow
+naming conventions that collide with the LAMMPS convention to append
+".bin" to a file name in order to switch to a binary output.  Thus for
+:doc:`vtk style dumps <dump_vtk>` the dump_modify command supports the
+keyword *binary* which selects between generating text mode and binary
+style VTK files.
+
+----------
+
 Restrictions
 """"""""""""
 

doc/src/fitpod_command.rst

@@ -1,18 +1,19 @@
 .. index:: fitpod
 
 fitpod command
-======================
+==============
 
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
-   fitpod Ta_param.pod Ta_data.pod
+   fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod
 
 * fitpod = style name of this command
 * Ta_param.pod = an input file that describes proper orthogonal descriptors (PODs)
 * Ta_data.pod = an input file that specifies DFT data used to fit a POD potential
+* Ta_coefficients.pod (optional) = an input file that specifies trainable coefficients of a POD potential
 
 Examples
 """"""""
@@ -20,20 +21,26 @@ Examples
 .. code-block:: LAMMPS
 
    fitpod Ta_param.pod Ta_data.pod
+   fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod
 
 Description
 """""""""""
 .. versionadded:: 22Dec2022
 
 Fit a machine-learning interatomic potential (ML-IAP) based on proper
-orthogonal descriptors (POD).  Two input files are required for this
+orthogonal descriptors (POD); please see :ref:`(Nguyen and Rohskopf)
-command. The first input file describes a POD potential parameter
+<Nguyen20222a>`, :ref:`(Nguyen2023) <Nguyen20232a>`, :ref:`(Nguyen2024)
-settings, while the second input file specifies the DFT data used for
+<Nguyen20242a>`, and :ref:`(Nguyen and Sema) <Nguyen20243a>` for details.
-the fitting procedure.
+The fitted POD potential can be used to run MD simulations via
+:doc:`pair_style pod <pair_pod>`.
 
-The table below has one-line descriptions of all the keywords that can
+Two input files are required for this command. The first input file
-be used in the first input file (i.e. ``Ta_param.pod`` in the example
+describes a POD potential parameter settings, while the second input
-above):
+file specifies the DFT data used for the fitting procedure. All keywords
+except *species* have default values. If a keyword is not set in the
+input file, its default value is used. The table below has one-line
+descriptions of all the keywords that can be used in the first input
+file (i.e. ``Ta_param.pod``)
 
 .. list-table::
    :header-rows: 1
@@ -52,7 +59,7 @@ above):
      - INT
      - three integer constants specify boundary conditions
    * - rin
-     - 1.0
+     - 0.5
      - REAL
      - a real number specifies the inner cut-off radius
    * - rcut
@@ -60,46 +67,75 @@ above):
      - REAL
      - a real number specifies the outer cut-off radius
    * - bessel_polynomial_degree
-     - 3
+     - 4
      - INT
      - the maximum degree of Bessel polynomials
    * - inverse_polynomial_degree
-     - 6
+     - 8
      - INT
      - the maximum degree of inverse radial basis functions
+   * - number_of_environment_clusters
+     - 1
+     - INT
+     - the number of clusters for environment-adaptive potentials
+   * - number_of_principal_components
+     - 2
+     - INT
+     - the number of principal components for dimensionality reduction
    * - onebody
      - 1
      - BOOL
      - turns on/off one-body potential
    * - twobody_number_radial_basis_functions
-     - 6
+     - 8
      - INT
      - number of radial basis functions for two-body potential
    * - threebody_number_radial_basis_functions
-     - 5
+     - 6
      - INT
      - number of radial basis functions for three-body potential
-   * - threebody_number_angular_basis_functions
+   * - threebody_angular_degree
      - 5
      - INT
-     - number of angular basis functions for three-body potential
+     - angular degree for three-body potential
-   * - fourbody_snap_twojmax
+   * - fourbody_number_radial_basis_functions
+     - 4
+     - INT
+     - number of radial basis functions for four-body potential
+   * - fourbody_angular_degree
+     - 3
+     - INT
+     - angular degree for four-body potential
+   * - fivebody_number_radial_basis_functions
      - 0
      - INT
-     - band limit for SNAP bispectrum components (0,2,4,6,8... allowed)
+     - number of radial basis functions for five-body potential
-   * - fourbody_snap_chemflag
+   * - fivebody_angular_degree
      - 0
-     - BOOL
+     - INT
-     - turns on/off the explicit multi-element variant of the SNAP bispectrum components
+     - angular degree for five-body potential
-   * - quadratic_pod_potential
+   * - sixbody_number_radial_basis_functions
      - 0
-     - BOOL
+     - INT
-     - turns on/off quadratic POD potential
+     - number of radial basis functions for six-body potential
+   * - sixbody_angular_degree
+     - 0
+     - INT
+     - angular degree for six-body potential
+   * - sevenbody_number_radial_basis_functions
+     - 0
+     - INT
+     - number of radial basis functions for seven-body potential
+   * - sevenbody_angular_degree
+     - 0
+     - INT
+     - angular degree for seven-body potential
+
+Note that both the number of radial basis functions and angular degree
+must decrease as the body order increases. The next table describes all
+keywords that can be used in the second input file (i.e. ``Ta_data.pod``
+in the example above):
 
-All keywords except *species* have default values. If a keyword is not
-set in the input file, its default value is used.  The next table
-describes all keywords that can be used in the second input file
-(i.e. ``Ta_data.pod`` in the example above):
 
 .. list-table::
    :header-rows: 1
@@ -125,6 +161,10 @@ describes all keywords that can be used in the second input file
      - ""
      - STRING
      - specifies the path to test data files in double quotes
+   * - path_to_environment_configuration_set
+     - ""
+     - STRING
+     - specifies the path to environment configuration files in double quotes
    * - fraction_training_data_set
      - 1.0
      - REAL
@@ -133,6 +173,14 @@ describes all keywords that can be used in the second input file
      - 0
      - BOOL
      - turns on/off randomization of the training set
+   * - fraction_test_data_set
+     - 1.0
+     - REAL
+     - a real number (<= 1.0) specifies the fraction of the test set used to validate POD
+   * - randomize_test_data_set
+     - 0
+     - BOOL
+     - turns on/off randomization of the test set
    * - fitting_weight_energy
      - 100.0
      - REAL
@@ -161,6 +209,10 @@ describes all keywords that can be used in the second input file
      - 8
      - INT
      - number of digits after the decimal points for numbers in the coefficient file
+   * - group_weights
+     - global
+     - STRING
+     - ``table`` uses group weights defined for each group named by filename
 
 All keywords except *path_to_training_data_set* have default values. If
 a keyword is not set in the input file, its default value is used.  After
@@ -172,14 +224,44 @@ successful training, a number of output files are produced, if enabled:
 * ``<basename>_test_analysis.pod`` reports detailed errors for all test configurations
 * ``<basename>_coefficients.pod`` contains the coefficients of the POD potential
 
-After training the POD potential, ``Ta_param.pod`` and ``<basename>_coefficients.pod``
+After training the POD potential, ``Ta_param.pod`` and
-are the two files needed to use the POD potential in LAMMPS. See
+``<basename>_coefficients.pod`` are the two files needed to use the POD
-:doc:`pair_style pod <pair_pod>` for using the POD potential. Examples
+potential in LAMMPS.  See :doc:`pair_style pod <pair_pod>` for using the
-about training and using POD potentials are found in the directory
+POD potential. Examples about training and using POD potentials are
-lammps/examples/PACKAGES/pod.
+found in the directory lammps/examples/PACKAGES/pod and the Github repo
+https://github.com/cesmix-mit/pod-examples.
 
-Parameterized Potential Energy Surface
+Loss Function Group Weights
-""""""""""""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The *group_weights* keyword in the ``data.pod`` file is responsible for
+weighting certain groups of configurations in the loss function. For
+example:
+
+.. code-block:: LAMMPS
+
+    group_weights table
+    Displaced_A15 100.0 1.0
+    Displaced_BCC 100.0 1.0
+    Displaced_FCC 100.0 1.0
+    Elastic_BCC   100.0 1.0
+    Elastic_FCC   100.0 1.0
+    GSF_110       100.0 1.0
+    GSF_112       100.0 1.0
+    Liquid        100.0 1.0
+    Surface       100.0 1.0
+    Volume_A15    100.0 1.0
+    Volume_BCC    100.0 1.0
+    Volume_FCC    100.0 1.0
+
+This will apply an energy weight of ``100.0`` and a force weight of
+``1.0`` for all groups in the ``Ta`` example. The groups are named by
+their respective filename. If certain groups are left out of this table,
+then the globally defined weights from the ``fitting_weight_energy`` and
+``fitting_weight_force`` keywords will be used.
+
+POD Potential
+"""""""""""""
 
 We consider a multi-element system of *N* atoms with :math:`N_{\rm e}`
 unique elements.  We denote by :math:`\boldsymbol r_n` and :math:`Z_n`
@@ -187,535 +269,82 @@ position vector and type of an atom *n* in the system,
 respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_{\rm e}
 \}`, :math:`\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots,
 \boldsymbol r_N) \in \mathbb{R}^{3N}`, and :math:`\boldsymbol Z = (Z_1,
-Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The potential energy surface
+Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The total energy of the
-(PES) of the system can be expressed as a many-body expansion of the
+POD potential is expressed as :math:`E(\boldsymbol R, \boldsymbol Z) =
-form
+\sum_{i=1}^N E_i(\boldsymbol R_i, \boldsymbol Z_i)`, where
 
 .. math::
 
-    E(\boldsymbol R, \boldsymbol Z, \boldsymbol{\eta}, \boldsymbol{\mu}) \ = \ & \sum_{i} V^{(1)}(\boldsymbol r_i, Z_i, \boldsymbol \mu^{(1)} ) + \frac12 \sum_{i,j} V^{(2)}(\boldsymbol r_i, \boldsymbol r_j, Z_i, Z_j, \boldsymbol \eta, \boldsymbol \mu^{(2)})  \\
+    E_i(\boldsymbol R_i, \boldsymbol Z_i) \ = \ \sum_{m=1}^M c_m \mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)
-    & + \frac16 \sum_{i,j,k} V^{(3)}(\boldsymbol r_i, \boldsymbol r_j, \boldsymbol r_k, Z_i, Z_j, Z_k, \boldsymbol \eta, \boldsymbol \mu^{(3)}) + \ldots
+
-
+
-where :math:`V^{(1)}` is the one-body potential often used for
+Here :math:`c_m` are trainable coefficients and
-representing external field or energy of isolated elements, and the
+:math:`\mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)` are per-atom
-higher-body potentials :math:`V^{(2)}, V^{(3)}, \ldots` are symmetric,
+POD descriptors. Summing the per-atom descriptors over :math:`i` yields
-uniquely defined, and zero if two or more indices take identical values.
+the global descriptors :math:`d_m(\boldsymbol R, \boldsymbol Z) =
-The superscript on each potential denotes its body order. Each *q*-body
+\sum_{i=1}^N \mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)`.  It
-potential :math:`V^{(q)}` depends on :math:`\boldsymbol \mu^{(q)}` which
+thus follows that :math:`E(\boldsymbol R, \boldsymbol Z) = \sum_{m=1}^M
-are sets of parameters to fit the PES. Note that :math:`\boldsymbol \mu`
+c_m d_m(\boldsymbol R, \boldsymbol Z)`.
-is a collection of all potential parameters :math:`\boldsymbol
+
-\mu^{(1)}`, :math:`\boldsymbol \mu^{(2)}`, :math:`\boldsymbol
+The per-atom POD descriptors include one, two, three, four, five, six,
-\mu^{(3)}`, etc, and that :math:`\boldsymbol \eta` is a set of
+and seven-body descriptors, which can be specified in the first input
-hyper-parameters such as inner cut-off radius :math:`r_{\rm in}` and
+file. Furthermore, the per-atom POD descriptors also depend on the
-outer cut-off radius :math:`r_{\rm cut}`.
+number of environment clusters specified in the first input file.
-
+Please see :ref:`(Nguyen2024) <Nguyen20242a>` and :ref:`(Nguyen and Sema)
-Interatomic potentials rely on parameters to learn relationship between
+<Nguyen20243a>` for the detailed description of the per-atom POD
-atomic environments and interactions.  Since interatomic potentials are
+descriptors.
-approximations by nature, their parameters need to be set to some
-reference values or fitted against data by necessity.  Typically,
-potential fitting finds optimal parameters, :math:`\boldsymbol \mu^*`,
-to minimize a certain loss function of the predicted quantities and
-data. Since the fitted potential depends on the data set used to fit it,
-different data sets will yield different optimal parameters and thus
-different fitted potentials. When fitting the same functional form on
-*Q* different data sets, we would obtain *Q* different optimized
-potentials, :math:`E(\boldsymbol R,\boldsymbol Z, \boldsymbol \eta,
-\boldsymbol \mu_q^*), 1 \le q \le Q`.  Consequently, there exist many
-different sets of optimized parameters for empirical interatomic
-potentials.
-
-Instead of optimizing the potential parameters, inspired by the reduced
-basis method :ref:`(Grepl) <Grepl20072>` for parameterized partial
-differential equations, we view the parameterized PES as a parametric
-manifold of potential energies
-
-.. math::
-
-    \mathcal{M} = \{E(\boldsymbol R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu) \ | \  \boldsymbol \mu \in \Omega^{\boldsymbol \mu} \}
-
-where :math:`\Omega^{\boldsymbol \mu}` is a parameter domain in which
-:math:`\boldsymbol \mu` resides.  The parametric manifold
-:math:`\mathcal{M}` contains potential energy surfaces for all values of
-:math:`\boldsymbol \mu \in \Omega^{\boldsymbol \mu}`.  Therefore, the
-parametric manifold yields a much richer and more transferable atomic
-representation than any particular individual PES :math:`E(\boldsymbol
-R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu^*)`.
-
-We propose specific forms of the parameterized potentials for one-body,
-two-body, and three-body interactions. We apply the Karhunen-Loeve
-expansion to snapshots of the parameterized potentials to obtain sets of
-orthogonal basis functions. These basis functions are aggregated
-according to the chemical elements of atoms, thus leading to
-multi-element proper orthogonal descriptors.
-
-Proper Orthogonal Descriptors
-"""""""""""""""""""""""""""""
-
-Proper orthogonal descriptors are finger prints characterizing the
-radial and angular distribution of a system of atoms. The detailed
-mathematical definition is given in the paper by Nguyen and Rohskopf
-:ref:`(Nguyen) <Nguyen20222>`.
-
-The descriptors for the one-body interaction are used to capture energy
-of isolated elements and defined as follows
-
-.. math::
-
-    D_{ip}^{(1)} =  \left\{
-        \begin{array}{ll}
-        1, & \mbox{if } Z_i = p \\
-        0, & \mbox{if } Z_i \neq p
-        \end{array}
-    \right.
-
-for :math:`1 \le i \le N, 1 \le p \le N_{\rm e}`. The number of one-body
-descriptors per atom is equal to the number of elements. The one-body
-descriptors are independent of atom positions, but dependent on atom
-types. The one-body descriptors are active only when the keyword
-*onebody* is set to 1.
-
-We adopt the usual assumption that the direct interaction between two
-atoms vanishes smoothly when their distance is greater than the outer
-cutoff distance :math:`r_{\rm cut}`. Furthermore, we assume that two
-atoms can not get closer than the inner cutoff distance :math:`r_{\rm
-in}` due to the Pauli repulsion principle. Let :math:`r \in (r_{\rm in},
-r_{\rm cut})`, we introduce the following parameterized radial functions
-
-.. math::
-
-    \phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta)  = \frac{\sin (\alpha \pi x) }{r - r_{\rm in}}, \qquad  \varphi(r, \gamma)  = \frac{1}{r^\gamma} ,
-
-where the scaled distance function :math:`x` is defined below to enrich the two-body manifold
-
-.. math::
-
-    x(r, r_{\rm in}, r_{\rm cut}, \beta) = \frac{e^{-\beta(r - r_{\rm in})/(r_{\rm cut} - r_{\rm in})} - 1}{e^{-\beta} - 1} .
-
-We introduce the following function as a convex combination of the two functions
-
-.. math::
-
-    \psi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta, \gamma, \kappa)  = \kappa \phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) + (1- \kappa)  \varphi(r, \gamma) .
-
-We see that :math:`\psi` is a function of distance :math:`r`, cut-off
-distances :math:`r_{\rm in}` and :math:`r_{\rm cut}`, and parameters
-:math:`\alpha, \beta, \gamma, \kappa`. Together these parameters allow
-the function :math:`\psi` to characterize a diverse spectrum of two-body
-interactions within the cut-off interval :math:`(r_{\rm in}, r_{\rm
-cut})`.
-
-Next, we introduce the following parameterized potential
-
-.. math::
-
-    W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)})  = f_{\rm c}(r_{ij}, \boldsymbol \eta) \psi(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)})
-
-where :math:`\eta_1 = r_{\rm in}, \eta_2 = r_{\rm cut}, \mu_1^{(2)} =
-\alpha, \mu_2^{(2)} = \beta, \mu_3^{(2)} = \gamma`, and
-:math:`\mu_4^{(2)} = \kappa`. Here the cut-off function :math:`f_{\rm
-c}(r_{ij}, \boldsymbol \eta)` proposed in [refs] is used to ensure the
-smooth vanishing of the potential and its derivative for :math:`r_{ij}
-\ge r_{\rm cut}`:
-
-.. math::
-
-    f_{\rm c}(r_{ij},  r_{\rm in}, r_{\rm cut})  =  \exp \left(1 -\frac{1}{\sqrt{\left(1 - \frac{(r-r_{\rm in})^3}{(r_{\rm cut} - r_{\rm in})^3} \right)^2 + 10^{-6}}} \right)
-
-Based on the parameterized potential, we form a set of snapshots as
-follows.  We assume that we are given :math:`N_{\rm s}` parameter tuples
-:math:`\boldsymbol \mu^{(2)}_\ell, 1 \le \ell \le N_{\rm s}`. We
-introduce the following set of snapshots on :math:`(r_{\rm in}, r_{\rm
-cut})`:
-
-.. math::
-
-    \xi_\ell(r_{ij}, \boldsymbol \eta) =  W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}_\ell),  \quad \ell = 1, \ldots, N_{\rm s} .
-
-To ensure adequate sampling of the PES for different parameters, we
-choose :math:`N_{\rm s}` parameter points :math:`\boldsymbol
-\mu^{(2)}_\ell = (\alpha_\ell, \beta_\ell, \gamma_\ell, \kappa_\ell), 1
-\le \ell \le N_{\rm s}` as follows. The parameters :math:`\alpha \in [1,
-N_\alpha]` and :math:`\gamma \in [1, N_\gamma]` are integers, where
-:math:`N_\alpha` and :math:`N_\gamma` are the highest degrees for
-:math:`\alpha` and :math:`\gamma`, respectively. We next choose
-:math:`N_\beta` different values of :math:`\beta` in the interval
-:math:`[\beta_{\min}, \beta_{\max}]`, where :math:`\beta_{\min} = 0` and
-:math:`\beta_{\max} = 4`. The parameter :math:`\kappa` can be set either
-0 or 1.  Hence, the total number of parameter points is :math:`N_{\rm s}
-= N_\alpha N_\beta + N_\gamma`.  Although :math:`N_\alpha, N_\beta,
-N_\gamma` can be chosen conservatively large, we find that
-:math:`N_\alpha = 6, N_\beta = 3, N_\gamma = 8` are adequate for most
-problems.  Note that :math:`N_\alpha` and :math:`N_\gamma` correspond to
-*bessel_polynomial_degree* and *inverse_polynomial_degree*,
-respectively.
-
-We employ the Karhunen-Loeve (KL) expansion to generate an orthogonal
-basis set which is known to be optimal for representation of the
-snapshot family :math:`\{\xi_\ell\}_{\ell=1}^{N_{\rm s}}`. The two-body
-orthogonal basis functions are computed as follows
-
-.. math::
-
-    U^{(2)}_m(r_{ij}, \boldsymbol \eta) = \sum_{\ell = 1}^{N_{\rm s}} A_{\ell m}(\boldsymbol \eta) \,  \xi_\ell(r_{ij}, \boldsymbol \eta), \qquad m = 1, \ldots, N_{\rm 2b} ,
-
-where the matrix :math:`\boldsymbol A \in \mathbb{R}^{N_{\rm s} \times
-N_{\rm s}}` consists of eigenvectors of the eigenvalue problem
-
-.. math::
-
-    \boldsymbol C \boldsymbol a = \lambda \boldsymbol a
-
-with the entries of :math:`\boldsymbol C \in \mathbb{R}^{N_{\rm s} \times N_{\rm s}}` being given by
-
-.. math::
-
-    C_{ij}  = \frac{1}{N_{\rm s}} \int_{r_{\rm in}}^{r_{\rm cut}} \xi_i(x, \boldsymbol \eta) \xi_j(x, \boldsymbol \eta) dx, \quad 1 \le i, j \le N_{\rm s}
-
-Note that the eigenvalues :math:`\lambda_\ell, 1 \le \ell \le N_{\rm
-s}`, are ordered such that :math:`\lambda_1 \ge \lambda_2 \ge \ldots \ge
-\lambda_{N_{\rm s}}`, and that the matrix :math:`\boldsymbol A` is
-pe-computed and stored for any given :math:`\boldsymbol \eta`.  Owing to
-the rapid convergence of the KL expansion, only a small number of
-orthogonal basis functions is needed to obtain accurate
-approximation. The value of :math:`N_{\rm 2b}` corresponds to
-*twobody_number_radial_basis_functions*.
-
-The two-body proper orthogonal descriptors at each atom *i* are computed
-by summing the orthogonal basis functions over the neighbors of atom *i*
-and numerating on the atom types as follows
-
-.. math::
-
-    D^{(2)}_{im l(p, q) }(\boldsymbol \eta)  = \left\{
-    \begin{array}{ll}
-    \displaystyle \sum_{\{j | Z_j = q\}} U^{(2)}_m(r_{ij},  \boldsymbol \eta), & \mbox{if } Z_i = p \\
-    0, & \mbox{if } Z_i \neq p
-    \end{array}
-    \right.
-
-for :math:`1 \le i \le N, 1 \le m \le N_{\rm 2b}, 1 \le q, p \le N_{\rm
-e}`. Here :math:`l(p,q)` is a symmetric index mapping such that
-
-.. math::
-
-    l(p,q)  = \left\{
-    \begin{array}{ll}
-    q + (p-1) N_{\rm e} - p(p-1)/2, & \mbox{if } q \ge p \\
-    p + (q-1) N_{\rm e} - q(q-1)/2, & \mbox{if } q < p .
-    \end{array}
-    \right.
-
-The number of two-body descriptors per atom is thus :math:`N_{\rm 2b}
-N_{\rm e}(N_{\rm e}+1)/2`.
-
-It is important to note that the orthogonal basis functions do not
-depend on the atomic numbers :math:`Z_i` and :math:`Z_j`. Therefore, the
-cost of evaluating the basis functions and their derivatives with
-respect to :math:`r_{ij}` is independent of the number of elements
-:math:`N_{\rm e}`. Consequently, even though the two-body proper
-orthogonal descriptors depend on :math:`\boldsymbol Z`, their
-computational complexity is independent of :math:`N_{\rm e}`.
-
-In order to provide proper orthogonal descriptors for three-body
-interactions, we need to introduce a three-body parameterized
-potential. In particular, the three-body potential is defined as a
-product of radial and angular functions as follows
-
-.. math::
-
-    W^{(3)}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta, \boldsymbol \mu^{(3)})  =  \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}) \\
-    \psi(r_{ik}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ik}, r_{\rm min}, r_{\rm max}) \\
-    \cos (\sigma \theta_{ijk} + \zeta)
-
-where :math:`\sigma` is the periodic multiplicity, :math:`\zeta` is the
-equilibrium angle, :math:`\boldsymbol \mu^{(3)} = (\alpha, \beta,
-\gamma, \kappa, \sigma, \zeta)`. The three-body potential provides an
-angular fingerprint of the atomic environment through the bond angles
-:math:`\theta_{ijk}` formed with each pair of neighbors :math:`j` and
-:math:`k`.  Compared to the two-body potential, the three-body potential
-has two extra parameters :math:`(\sigma, \zeta)` associated with the
-angular component.
-
-Let :math:`\boldsymbol \varrho = (\alpha, \beta, \gamma, \kappa)`. We
-assume that we are given :math:`L_{\rm r}` parameter tuples
-:math:`\boldsymbol \varrho_\ell, 1 \le \ell \le L_{\rm r}`.  We
-introduce the following set of snapshots on :math:`(r_{\min},
-r_{\max})`:
-
-.. math::
-
-    \zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ) =  \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \boldsymbol \varrho_\ell) f_{\rm c}(r_{ij}, r_{\rm min},  r_{\rm max}), \quad 1 \le \ell \le L_{\rm r} .
-
-We apply the Karhunen-Loeve (KL) expansion to this set of snapshots to
-obtain orthogonal basis functions as follows
-
-.. math::
-
-    U^{r}_m(r_{ij}, r_{\rm min}, r_{\rm max} ) = \sum_{\ell = 1}^{L_{\rm r}} A_{\ell m} \,  \zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ), \qquad m = 1, \ldots, N_{\rm r} ,
-
-where the matrix :math:`\boldsymbol A \in \mathbb{R}^{L_{\rm r} \times L_{\rm r}}` consists
-of eigenvectors of the eigenvalue problem. For the parameterized angular function,
-we consider angular basis functions
-
-.. math::
-
-    U^{a}_n(\theta_{ijk}) = \cos ((n-1) \theta_{ijk}), \qquad  n = 1,\ldots, N_{\rm a},
-
-where :math:`N_{\rm a}` is the number of angular basis functions. The orthogonal
-basis functions for the parameterized potential are computed as follows
-
-.. math::
-
-    U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta) = U^{r}_m(r_{ij}, \boldsymbol \eta) U^{r}_m(r_{ik}, \boldsymbol \eta) U^{a}_n(\theta_{ijk}),
-
-for :math:`1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}`. The number of three-body
-orthogonal basis functions is equal to :math:`N_{\rm 3b} = N_{\rm r} N_{\rm a}` and
-independent of the number of elements. The value of :math:`N_{\rm r}` corresponds to
-*threebody_number_radial_basis_functions*, while that of :math:`N_{\rm a}` to
-*threebody_number_angular_basis_functions*.
-
-The three-body proper orthogonal descriptors at each atom *i*
-are obtained by summing over the neighbors *j* and *k* of atom *i* as
-
-.. math::
-
-    D^{(3)}_{imn \ell(p, q, s)}(\boldsymbol \eta)  = \left\{
-    \begin{array}{ll}
-    \displaystyle \sum_{\{j | Z_j = q\}} \sum_{\{k | Z_k = s\}} U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta), & \mbox{if } Z_i = p \\
-    0, & \mbox{if } Z_i \neq p
-    \end{array}
-    \right.
-
-for :math:`1 \le i \le N, 1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}, 1 \le q, p, s \le N_{\rm e}`,
-where
-
-.. math::
-
-    \ell(p,q,s)  = \left\{
-    \begin{array}{ll}
-    s + (q-1) N_{\rm e} - q(q-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2 , & \mbox{if } s \ge q \\
-    q + (s-1) N_{\rm e} - s(s-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2, & \mbox{if } s < q .
-    \end{array}
-    \right.
-
-The number of three-body descriptors per atom is thus :math:`N_{\rm 3b} N_{\rm e}^2(N_{\rm e}+1)/2`.
-While the number of three-body PODs is cubic function of the number of elements,
-the computational complexity of the three-body PODs is independent of the number of elements.
-
-Four-Body SNAP Descriptors
-""""""""""""""""""""""""""
-
-In addition to the proper orthogonal descriptors described above, we also employ
-the spectral neighbor analysis potential (SNAP) descriptors. SNAP uses bispectrum components
-to characterize the local neighborhood of each atom in a very general way. The mathematical definition
-of the bispectrum calculation and its derivatives w.r.t. atom positions is described in
-:doc:`compute snap <compute_sna_atom>`. In SNAP, the
-total energy is decomposed into a sum over atom energies. The energy of
-atom *i* is expressed as a weighted sum over bispectrum components.
-
-.. math::
-
-   E_i^{\rm SNAP} = \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)}
-
-
-where the SNAP descriptors are related to the bispectrum components by
-
-.. math::
-
-    D^{(4)}_{ikp}  = \left\{
-    \begin{array}{ll}
-    \displaystyle B_{ik}, & \mbox{if } Z_i = p \\
-    0, & \mbox{if } Z_i \neq p
-    \end{array}
-    \right.
-
-Here :math:`B_{ik}` is the *k*\ -th bispectrum component of atom *i*. The number of
-bispectrum components :math:`N_{\rm 4b}` depends on the value of *fourbody_snap_twojmax* :math:`= 2 J_{\rm max}`
-and *fourbody_snap_chemflag*. If *fourbody_snap_chemflag* = 0
-then :math:`N_{\rm 4b} = (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`.
-If *fourbody_snap_chemflag* = 1 then :math:`N_{\rm 4b} = N_{\rm e}^3 (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`.
-The bispectrum calculation is described in more detail in :doc:`compute sna/atom <compute_sna_atom>`.
-
-Linear Proper Orthogonal Descriptor Potentials
-""""""""""""""""""""""""""""""""""""""""""""""
-
-The proper orthogonal descriptors and SNAP descriptors are used to define the atomic energies
-in the following expansion
-
-.. math::
-
-    E_{i}(\boldsymbol \eta) = \sum_{p=1}^{N_{\rm e}} c^{(1)}_p D^{(1)}_{ip} + \sum_{m=1}^{N_{\rm 2b}}  \sum_{l=1}^{N_{\rm e}(N_{\rm e}+1)/2} c^{(2)}_{ml} D^{(2)}_{iml}(\boldsymbol \eta) + \sum_{m=1}^{N_{\rm r}} \sum_{n=1}^{N_{\rm a}}  \sum_{\ell=1}^{N_{\rm e}^2(N_{\rm e}+1)/2} c^{(3)}_{mn\ell} D^{(3)}_{imn\ell}(\boldsymbol \eta) + \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)}(\boldsymbol \eta),
-
-where :math:`D^{(1)}_{ip}, D^{(2)}_{iml}, D^{(3)}_{imn\ell}, D^{(4)}_{ikp}` are the  one-body, two-body, three-body, four-body descriptors,
-respectively, and :math:`c^{(1)}_p, c^{(2)}_{ml}, c^{(3)}_{mn\ell}, c^{(4)}_{kp}` are their respective expansion
-coefficients. In a more compact notation that implies summation over descriptor indices
-the atomic energies can be written as
-
-.. math::
-
-    E_i(\boldsymbol \eta) =  \sum_{m=1}^{N_{\rm e}} c^{(1)}_m D^{(1)}_{im} +  \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_k D^{(2)}_{im} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m D^{(3)}_{im} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m D^{(4)}_{im}
-
-where :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2`,
-:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2`, and
-:math:`N_{\rm d}^{(4)} = N_{\rm 4b} N_{\rm e}` are
-the number of two-body, three-body, and four-body descriptors, respectively.
-
-The potential energy is then obtained by summing local atomic energies :math:`E_i`
-for all atoms :math:`i` in the system
-
-.. math::
-
-    E(\boldsymbol \eta) = \sum_{i}^N E_{i}(\boldsymbol \eta)
-
-Because the descriptors are one-body, two-body, and three-body terms,
-the resulting POD potential is a three-body PES. We can express the potential
-energy as a linear combination of the global descriptors as follows
-
-.. math::
-
-    E(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m d^{(1)}_{m} +  \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m d^{(2)}_{m} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m d^{(3)}_{m} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m d^{(4)}_{m}
-
-where  the global descriptors are given by
-
-.. math::
-
-    d_{m}^{(1)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(1)}(\boldsymbol \eta), \quad d_{m}^{(2)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(2)}(\boldsymbol \eta), \quad d_{m}^{(3)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(3)}(\boldsymbol \eta), \quad d_{m}^{(4)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(4)}(\boldsymbol \eta)
-
-Hence, we obtain the atomic forces as
-
-.. math::
-
-    \boldsymbol F = -\nabla E(\boldsymbol \eta) = - \sum_{m=1}^{N_{\rm d}^{(2)}}  c^{(2)}_m  \nabla d_m^{(2)} - \sum_{m=1}^{N_{\rm d}^{(3)}}  c^{(3)}_m \nabla d_m^{(3)} - \sum_{m=1}^{N_{\rm d}^{(4)}}  c^{(4)}_m \nabla d_m^{(4)}
-
-where :math:`\nabla d_m^{(2)}`, :math:`\nabla d_m^{(3)}` and :math:`\nabla d_m^{(4)}` are derivatives of the two-body
-three-body, and four-body global descriptors with respect to atom positions, respectively.
-Note that since the first-body global descriptors are constant, their derivatives are zero.
-
-Quadratic Proper Orthogonal Descriptor Potentials
-"""""""""""""""""""""""""""""""""""""""""""""""""
-
-We recall two-body PODs :math:`D^{(2)}_{ik}, 1 \le k \le N_{\rm d}^{(2)}`,
-and three-body PODs :math:`D^{(3)}_{im}, 1 \le m \le N_{\rm d}^{(3)}`,
-with :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2` and
-:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2` being
-the number of descriptors per atom for the two-body PODs and three-body PODs,
-respectively. We employ them to define a new set of atomic descriptors as follows
-
-.. math::
-
-    D^{(2*3)}_{ikm} = \frac{1}{2N}\left( D^{(2)}_{ik} \sum_{j=1}^N D^{(3)}_{jm} + D^{(3)}_{im} \sum_{j=1}^N D^{(2)}_{jk}  \right)
-
-for :math:`1 \le i \le N, 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`.
-The new descriptors are four-body because they involve central atom :math:`i` together
-with three neighbors :math:`j, k` and :math:`l`. The total number of new  descriptors per atom is equal to
-
-.. math::
-
-    N_{\rm d}^{(2*3)} = N_{\rm d}^{(2)} * N_{\rm d}^{(3)} = N_{\rm 2b} N_{\rm 3b} N_{\rm e}^3 (N_{\rm e}+1)^2/4 .
-
-The new global descriptors are calculated as
-
-.. math::
-
-    d^{(2*3)}_{km} = \sum_{i=1}^N D^{(2*3)}_{ikm} = \left( \sum_{i=1}^N D^{(2)}_{ik} \right) \left( \sum_{i=1}^N D^{(3)}_{im} \right) = d^{(2)}_{k} d^{(3)}_m,
-
-for :math:`1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`. Hence, the gradient
-of the new global descriptors with respect to atom positions is calculated as
-
-.. math::
-
-    \nabla d^{(2*3)}_{km} = d^{(3)}_m \nabla d^{(2)}_{k}  +  d^{(2)}_{k} \nabla d^{(3)}_m, \quad 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)} .
-
-The quadratic  POD potential is defined as a linear combination of the
-original and new global descriptors as follows
-
-.. math::
-
-    E^{(2*3)} = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d^{(2*3)}_{km} .
-
-It thus follows that
-
-.. math::
-
-    E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \left( \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)} \right) d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} \left( \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)} \right) d_m^{(3)}  ,
-
-which is simplified to
-
-.. math::
-
-    E^{(2*3)} =  0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b_k^{(2)} d_k^{(2)} +  0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}}   b_m^{(3)} d_m^{(3)}
-
-where
-
-.. math::
-
-    b_k^{(2)} & = \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)}, \quad k = 1,\ldots, N_{\rm 2d}^{(2*3)}, \\
-    b_m^{(3)} & = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)}, \quad m = 1,\ldots, N_{\rm 3d}^{(2*3)} .
-
-The quadratic POD potential results in the following atomic forces
-
-.. math::
-
-    \boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km}  \nabla d^{(2*3)}_{km} .
-
-It can be shown that
-
-.. math::
-
-    \boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}}   b^{(2)}_k \nabla d_k^{(2)} - \sum_{m=1}^{N_{\rm 3d}^{(2*3)}}  b^{(3)}_m  \nabla d_m^{(3)} .
-
-The calculation of the atomic forces for the quadratic POD  potential
-only requires the extra calculation of :math:`b_k^{(2)}` and :math:`b_m^{(3)}` which can be negligible.
-As a result, the quadratic  POD potential does not increase the computational complexity.
-
 
 Training
 """"""""
 
-POD potentials are trained using the least-squares regression against
+A POD potential is trained using the least-squares regression against
 density functional theory (DFT) data.  Let :math:`J` be the number of
 training configurations, with :math:`N_j` being the number of atoms in
-the j-th configuration. Let :math:`\{E^{\star}_j\}_{j=1}^{J}` and
+the j-th configuration. The training configurations are extracted from
-:math:`\{\boldsymbol F^{\star}_j\}_{j=1}^{J}` be the DFT energies and
+the extended XYZ files located in a directory (i.e.,
-forces for :math:`J` configurations. Next, we calculate the global
+path_to_training_data_set in the second input file).  Let
-descriptors and their derivatives for all training configurations. Let
+:math:`\{E^{\star}_j\}_{j=1}^{J}` and :math:`\{\boldsymbol
-:math:`d_{jm}, 1 \le m \le M`, be the global descriptors associated with
+F^{\star}_j\}_{j=1}^{J}` be the DFT energies and forces for :math:`J`
-the j-th configuration, where :math:`M` is the number of global
+configurations. Next, we calculate the global descriptors and their
-descriptors. We then form a matrix :math:`\boldsymbol A \in
+derivatives for all training configurations. Let :math:`d_{jm}, 1 \le m
-\mathbb{R}^{J \times M}` with entries :math:`A_{jm} = d_{jm}/ N_j` for
+\le M`, be the global descriptors associated with the j-th
-:math:`j=1,\ldots,J` and :math:`m=1,\ldots,M`.  Moreover, we form a
+configuration, where :math:`M` is the number of global descriptors. We
-matrix :math:`\boldsymbol B \in \mathbb{R}^{\mathcal{N} \times M}` by
+then form a matrix :math:`\boldsymbol A \in \mathbb{R}^{J \times M}`
-stacking the derivatives of the global descriptors for all training
+with entries :math:`A_{jm} = d_{jm}/ N_j` for :math:`j=1,\ldots,J` and
-configurations from top to bottom, where :math:`\mathcal{N} =
+:math:`m=1,\ldots,M`.  Moreover, we form a matrix :math:`\boldsymbol B
-3\sum_{j=1}^{J} N_j`.
+\in \mathbb{R}^{\mathcal{N} \times M}` by stacking the derivatives of
+the global descriptors for all training configurations from top to
+bottom, where :math:`\mathcal{N} = 3\sum_{j=1}^{J} N_j`.
 
 The coefficient vector :math:`\boldsymbol c` of the POD potential is
 found by solving the following least-squares problem
 
 .. math::
 
-    {\min}_{\boldsymbol c \in \mathbb{R}^{M}} \ w_E \|\boldsymbol A(\boldsymbol \eta) \boldsymbol c - \bar{\boldsymbol E}^{\star} \|^2 + w_F \|\boldsymbol B(\boldsymbol \eta) \boldsymbol c + \boldsymbol F^{\star} \|^2 + w_R \|\boldsymbol c \|^2,
+    {\min}_{\boldsymbol c \in \mathbb{R}^{M}} \ w_E \|\boldsymbol A \boldsymbol c - \bar{\boldsymbol E}^{\star} \|^2 + w_F \|\boldsymbol B \boldsymbol c + \boldsymbol F^{\star} \|^2 + w_R \|\boldsymbol c \|^2,
 
 where :math:`w_E` and :math:`w_F` are weights for the energy
 (*fitting_weight_energy*) and force (*fitting_weight_force*),
-respectively; and :math:`w_R` is the regularization parameter (*fitting_regularization_parameter*).  Here :math:`\bar{\boldsymbol E}^{\star} \in
+respectively; and :math:`w_R` is the regularization parameter
-\mathbb{R}^{J}` is a vector of with entries :math:`\bar{E}^{\star}_j =
+(*fitting_regularization_parameter*).  Here :math:`\bar{\boldsymbol
-E^{\star}_j/N_j` and :math:`\boldsymbol F^{\star}` is a vector of
+E}^{\star} \in \mathbb{R}^{J}` is a vector of with entries
-:math:`\mathcal{N}` entries obtained by stacking :math:`\{\boldsymbol
+:math:`\bar{E}^{\star}_j = E^{\star}_j/N_j` and :math:`\boldsymbol
-F^{\star}_j\}_{j=1}^{J}` from top to bottom.
+F^{\star}` is a vector of :math:`\mathcal{N}` entries obtained by
+stacking :math:`\{\boldsymbol F^{\star}_j\}_{j=1}^{J}` from top to
+bottom.
 
-The training procedure is the same for both the linear and quadratic POD
+Validation
-potentials.  However, since the quadratic POD potential has a
+""""""""""
-significantly larger number of the global descriptors, it is more
-expensive to train the linear POD potential. This is because the
-training of the quadratic POD potential still requires us to calculate
-and store the quadratic global descriptors and their
-gradient. Furthermore, the quadratic POD potential may require more
-training data in order to prevent over-fitting. In order to reduce the
-computational cost of fitting the quadratic POD potential and avoid
-over-fitting, we can use subsets of two-body and three-body PODs for
-constructing the new descriptors.
 
+POD potential can be validated on a test dataset in a directory
+specified by setting path_to_test_data_set in the second input file.  It
+is possible to validate the POD potential after the training is
+complete.  This is done by providing the coefficient file as an input to
+:doc:`fitpod <fitpod_command>`, for example,
+
+.. code-block:: LAMMPS
+
+   fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod
 
 Restrictions
 """"""""""""
@@ -727,7 +356,11 @@ LAMMPS was built with that package. See the :doc:`Build package
 Related commands
 """"""""""""""""
 
-:doc:`pair_style pod <pair_pod>`
+:doc:`pair_style pod <pair_pod>`,
+:doc:`compute pod/atom <compute_pod_atom>`,
+:doc:`compute podd/atom <compute_pod_atom>`,
+:doc:`compute pod/local <compute_pod_atom>`,
+:doc:`compute pod/global <compute_pod_atom>`
 
 Default
 """""""
@@ -736,10 +369,20 @@ The keyword defaults are also given in the description of the input files.
 
 ----------
 
-.. _Grepl20072:
+.. _Nguyen20222a:
 
-**(Grepl)** Grepl, Maday, Nguyen, and Patera, ESAIM: Mathematical Modelling and Numerical Analysis 41(3), 575-605, (2007).
+**(Nguyen and Rohskopf)** Nguyen and Rohskopf,  Journal of Computational Physics, 480, 112030, (2023).
+
+.. _Nguyen20232a:
+
+**(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023).
+
+.. _Nguyen20242a:
+
+**(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024).
+
+.. _Nguyen20243a:
+
+**(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
 
-.. _Nguyen20222:
 
-**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022).

doc/src/fix.rst

@@ -193,6 +193,7 @@ accelerated styles exist.
 * :doc:`adapt <fix_adapt>` - change a simulation parameter over time
 * :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
 * :doc:`addforce <fix_addforce>` - add a force to each atom
+* :doc:`add/heat <fix_add_heat>` - add a heat flux to each atom
 * :doc:`addtorque <fix_addtorque>` - add a torque to a group of atoms
 * :doc:`alchemy <fix_alchemy>` - perform an "alchemical transformation" between two partitions
 * :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>` - torsion/torsion terms in AMOEBA force field
@@ -369,6 +370,11 @@ accelerated styles exist.
 * :doc:`reaxff/species <fix_reaxff_species>` - write out ReaxFF molecule information
 * :doc:`recenter <fix_recenter>` - constrain the center-of-mass position of a group of atoms
 * :doc:`restrain <fix_restrain>` - constrain a bond, angle, dihedral
+* :doc:`rheo <fix_rheo>` - integrator for the RHEO package
+* :doc:`rheo/thermal <fix_rheo_thermal>` - thermal integrator for the RHEO package
+* :doc:`rheo/oxidation <fix_rheo_oxidation>` - create oxidation bonds for the RHEO package
+* :doc:`rheo/pressure <fix_rheo_pressure>` - pressure calculation for the RHEO package
+* :doc:`rheo/viscosity <fix_rheo_pressure>` - viscosity calculation for the RHEO package
 * :doc:`rhok <fix_rhok>` - add bias potential for long-range ordered systems
 * :doc:`rigid <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NVE integration
 * :doc:`rigid/meso <fix_rigid_meso>` - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body

doc/src/fix_add_heat.rst

@@ -0,0 +1,111 @@
+.. index:: fix add/heat
+
+fix add/heat command
+====================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID add/heat style args keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* add/heat = style name of this fix command
+* style = *constant* or *linear* or *quartic*
+
+  .. parsed-literal::
+
+       *constant* args = *rate*
+         *rate* = rate of heat flow (energy/time units)
+       *linear* args = :math:`T_{target}` *k*
+         :math:`T_{target}` = target temperature (temperature units)
+         *k* = prefactor (energy/(time*temperature) units)
+       *quartic* args = :math:`T_{target}` *k*
+         :math:`T_{target}` = target temperature (temperature units)
+         *k* = prefactor (energy/(time*temperature^4) units)
+
+* zero or more keyword/value pairs may be appended to args
+* keyword = *overwrite*
+
+  .. parsed-literal::
+
+       *overwrite* value = *yes* or *no*
+         *yes* = sets current heat flow of particle
+         *no* = adds to current heat flow of particle
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all add/heat constant v_heat
+   fix 1 all add/heat linear 10.0 1.0 overwrite yes
+
+Description
+"""""""""""
+
+This fix adds heat to particles with the temperature attribute every timestep.
+Note that this is an internal temperature of a particle intended for use with
+non-atomistic models like the discrete element method.
+
+For the *constant* style, heat is added at the specified rate. For the *linear* style,
+heat is added at a rate of :math:`k (T_{target} - T)` where :math:`k` is the
+specified prefactor, :math:`T_{target}` is the specified target temperature, and
+:math:`T` is the temperature of the atom. This may be more representative of a
+conductive process. For the *quartic* style, heat is added at a rate of
+:math:`k (T_{target}^4 - T^4)`, akin to radiative heat transfer.
+
+The rate or temperature can be can be specified as an equal-style or atom-style
+:doc:`variable <variable>`.  If the value is a variable, it should be
+specified as v_name, where name is the variable name.  In this case, the
+variable will be evaluated each time step, and its value will be used to
+determine the rate of heat added.
+
+Equal-style variables can specify formulas with various mathematical
+functions and include :doc:`thermo_style <thermo_style>` command
+keywords for the simulation box parameters, time step, and elapsed time
+to specify time-dependent heating.
+
+Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates to specify spatially-dependent heating.
+
+If the *overwrite* keyword is set to *yes*, this fix will set the total
+heat flow on a particle every timestep, overwriting contributions from pair
+styles or other fixes. If *overwrite* is *no*, this fix will add heat on
+top of other contributions.
+
+----------
+
+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.
+No global or per-atom quantities are stored by this fix for access 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 pair style is part of the GRANULAR package.  It is
+only enabled if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` page for more info.
+
+This fix requires that atoms store temperature and heat flow
+as defined by the :doc:`fix property/atom <fix_property_atom>` command.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix heat/flow <fix_heat_flow>`,
+:doc:`fix property/atom <fix_property_atom>`,
+:doc:`fix rheo/thermal <fix_rheo_thermal>`
+
+Default
+"""""""
+
+The default for the *overwrite* keyword is *no*

doc/src/fix_deform.rst

@@ -4,9 +4,6 @@
 fix deform command
 ==================
 
-:doc:`fix deform/pressure <fix_deform_pressure>` command
-========================================================
-
 Accelerator Variants: *deform/kk*
 
 Syntax
@@ -14,12 +11,11 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   fix ID group-ID fix_style N parameter style args ... keyword value ...
+   fix ID group-ID deform N parameter style args ... keyword value ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* fix_style = *deform* or *deform/pressure*
 * N = perform box deformation every this many timesteps
-* one or more parameter/style/args sequences of arguments may be appended
+* one or more parameter/args sequences may be appended
 
   .. parsed-literal::
 
@@ -46,12 +42,6 @@ Syntax
            *variable* values = v_name1 v_name2
              v_name1 = variable with name1 for box length change as function of time
              v_name2 = variable with name2 for change rate as function of time
-           *pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-             target = target pressure (pressure units)
-             gain = proportional gain constant (1/(time * pressure) or 1/time units)
-           *pressure/mean* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-             target = target pressure (pressure units)
-             gain = proportional gain constant (1/(time * pressure) or 1/time units)
 
        *xy*, *xz*, *yz* args = style value
          style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable*
@@ -64,8 +54,6 @@ Syntax
                  effectively an engineering shear strain rate
            *erate* value = R
              R = engineering shear strain rate (1/time units)
-           *erate/rescale* value = R (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-             R = engineering shear strain rate (1/time units)
            *trate* value = R
              R = true shear strain rate (1/time units)
            *wiggle* values = A Tp
@@ -74,9 +62,6 @@ Syntax
            *variable* values = v_name1 v_name2
              v_name1 = variable with name1 for tilt change as function of time
              v_name2 = variable with name2 for change rate as function of time
-           *pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-             target = target pressure (pressure units)
-             gain = proportional gain constant (1/(time * pressure) or 1/time units)
 
 * zero or more keyword/value pairs may be appended
 * keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure*
@@ -92,15 +77,6 @@ Syntax
        *units* value = *lattice* or *box*
          lattice = distances are defined in lattice units
          box = distances are defined in simulation box units
-       *couple* value = *none* or *xyz* or *xy* or *yz* or *xz* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-         couple pressure values of various dimensions
-       *vol/balance/p* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-         Modifies the behavior of the *volume* option to try and balance pressures
-       *max/rate* value = *rate* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-         rate = maximum strain rate for pressure control
-       *normalize/pressure* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
-         Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
-
 
 Examples
 """"""""
@@ -112,8 +88,6 @@ Examples
    fix 1 all deform 1 xy erate 0.001 remap v
    fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0
 
-See examples for :doc:`fix deform/pressure <fix_deform_pressure>` on its doc page
-
 Description
 """""""""""
 
@@ -123,17 +97,13 @@ run.  Orthogonal simulation boxes have 3 adjustable parameters
 adjustable parameters (x,y,z,xy,xz,yz).  Any or all of them can be
 adjusted independently and simultaneously.
 
-The fix deform command allows use of all the arguments listed above,
+The :doc:`fix deform/pressure <fix_deform_pressure>` command extends
-except those flagged as available ONLY for the :doc:`fix
+this command with additional keywords and arguments.  The rest of this
-deform/pressure <fix_deform_pressure>` command, which are
+page explains the options common to both commands.  The :doc:`fix
-pressure-based controls.  The fix deform/pressure command allows use
+deform/pressure <fix_deform_pressure>` page explains the options
-of all the arguments listed above.
+available ONLY with the fix deform/pressure command.  Note that a
-
+simulation can define only a single deformation command: fix deform or
-The rest of this doc page explains the options common to both
+fix deform/pressure.
-commands.  The :doc:`fix deform/pressure <fix_deform_pressure>` doc
-page explains the options available ONLY with the fix deform/pressure
-command.  Note that a simulation can define only a single deformation
-command: fix deform or fix deform/pressure.
 
 Both these fixes can be used to perform non-equilibrium MD (NEMD)
 simulations of a continuously strained system.  See the :doc:`fix
@@ -143,6 +113,24 @@ simulation of a continuously extended system (extensional flow) can be
 modeled using the :ref:`UEF package <PKG-UEF>` and its :doc:`fix
 commands <fix_nh_uef>`.
 
+.. admonition:: Inconsistent trajectories due to image flags
+   :class: warning
+
+   When running long simulations while shearing the box or using a high
+   shearing rate, it is possible that the image flags used for storing
+   unwrapped atom positions will "wrap around".  When LAMMPS is compiled
+   with the default settings, case image flags are limited to a range of
+   :math:`-512 \le i \le 511`, which will overflow when atoms starting
+   at zero image flag value have passed through a periodic box dimension
+   more than 512 times.
+
+   Changing the :ref:`size of LAMMPS integer types <size>` to the
+   "bigbig" setting can make this overflow much less likely, since it
+   increases the image flag value range to :math:`- 1,048,576 \le i \le
+   1\,048\,575`
+
+----------
+
 For the *x*, *y*, *z* parameters, the associated dimension cannot be
 shrink-wrapped.  For the *xy*, *yz*, *xz* parameters, the associated
 second dimension cannot be shrink-wrapped.  Dimensions not varied by

doc/src/fix_deform_pressure.rst

@@ -13,29 +13,66 @@ Syntax
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * deform/pressure = style name of this fix command
 * N = perform box deformation every this many timesteps
-* one or more parameter/arg sequences may be appended
+* one or more parameter/args sequences may be appended
 
   .. parsed-literal::
 
      parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *box*
        *x*, *y*, *z* args = style value(s)
          style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* or *pressure* or *pressure/mean*
+           *final* values = lo hi
+             lo hi = box boundaries at end of run (distance units)
+           *delta* values = dlo dhi
+             dlo dhi = change in box boundaries at end of run (distance units)
+           *scale* values = factor
+             factor = multiplicative factor for change in box length at end of run
+           *vel* value = V
+             V = change box length at this velocity (distance/time units),
+                 effectively an engineering strain rate
+           *erate* value = R
+             R = engineering strain rate (1/time units)
+           *trate* value = R
+             R = true strain rate (1/time units)
+           *volume* value = none = adjust this dim to preserve volume of system
+           *wiggle* values = A Tp
+             A = amplitude of oscillation (distance units)
+             Tp = period of oscillation (time units)
+           *variable* values = v_name1 v_name2
+             v_name1 = variable with name1 for box length change as function of time
+             v_name2 = variable with name2 for change rate as function of time
            *pressure* values = target gain
              target = target pressure (pressure units)
              gain = proportional gain constant (1/(time * pressure) or 1/time units)
            *pressure/mean* values = target gain
              target = target pressure (pressure units)
              gain = proportional gain constant (1/(time * pressure) or 1/time units)
-           NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
 
        *xy*, *xz*, *yz* args = style value
          style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure* or *erate/rescale*
+           *final* value = tilt
+             tilt = tilt factor at end of run (distance units)
+           *delta* value = dtilt
+             dtilt = change in tilt factor at end of run (distance units)
+           *vel* value = V
+             V = change tilt factor at this velocity (distance/time units),
+                 effectively an engineering shear strain rate
+           *erate* value = R
+             R = engineering shear strain rate (1/time units)
+           *erate/rescale* value = R
+             R = engineering shear strain rate (1/time units)
+           *trate* value = R
+             R = true shear strain rate (1/time units)
+           *wiggle* values = A Tp
+             A = amplitude of oscillation (distance units)
+             Tp = period of oscillation (time units)
+           *variable* values = v_name1 v_name2
+             v_name1 = variable with name1 for tilt change as function of time
+             v_name2 = variable with name2 for change rate as function of time
            *pressure* values = target gain
              target = target pressure (pressure units)
              gain = proportional gain constant (1/(time * pressure) or 1/time units)
            *erate/rescale* value = R
              R = engineering shear strain rate (1/time units)
-           NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
 
        *box* = style value
          style = *volume* or *pressure*
@@ -49,6 +86,15 @@ Syntax
 
   .. parsed-literal::
 
+       *remap* value = *x* or *v* or *none*
+         x = remap coords of atoms in group into deforming box
+         v = remap velocities of atoms in group when they cross periodic boundaries
+         none = no remapping of x or v
+       *flip* value = *yes* or *no*
+         allow or disallow box flips when it becomes highly skewed
+       *units* value = *lattice* or *box*
+         lattice = distances are defined in lattice units
+         box = distances are defined in simulation box units
        *couple* value = *none* or *xyz* or *xy* or *yz* or *xz*
          couple pressure values of various dimensions
        *vol/balance/p* value = *yes* or *no*
@@ -57,7 +103,6 @@ Syntax
          rate = maximum strain rate for pressure control
        *normalize/pressure* value = *yes* or *no*
          Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
-       NOTE: All other keywords are documented by the :doc:`fix deform <fix_deform>` command
 
 Examples
 """"""""
@@ -79,10 +124,26 @@ pressure-based controls implemented by this command.
 
 All arguments described on the :doc:`fix deform <fix_deform>` doc page
 also apply to this fix unless otherwise noted below.  The rest of this
-doc page explains the arguments specific to this fix.  Note that a
+page explains the arguments specific to this fix only.  Note that a
 simulation can define only a single deformation command: fix deform or
 fix deform/pressure.
 
+.. admonition:: Inconsistent trajectories due to image flags
+   :class: warning
+
+   When running long simulations while shearing the box or using a high
+   shearing rate, it is possible that the image flags used for storing
+   unwrapped atom positions will "wrap around".  When LAMMPS is compiled
+   with the default settings, case image flags are limited to a range of
+   :math:`-512 \le i \le 511`, which will overflow when atoms starting
+   at zero image flag value have passed through a periodic box dimension
+   more than 512 times.
+
+   Changing the :ref:`size of LAMMPS integer types <size>` to the
+   "bigbig" setting can make this overflow much less likely, since it
+   increases the image flag value range to :math:`- 1,048,576 \le i \le
+   1\,048\,575`
+
 ----------
 
 For the *x*, *y*, and *z* parameters, this is the meaning of the

doc/src/fix_electrode.rst

@@ -38,7 +38,7 @@ Syntax
        *electrode/thermo* args = potential eta *temp* values
             potential = electrode potential
             charge = electrode charge
-            eta = reciprocal width of electrode charge smearing
+            eta = reciprocal width of electrode charge smearing (can be NULL if eta keyword is used)
             *temp* values = T_v tau_v rng_v
                 T_v = temperature of thermo-potentiostat
                 tau_v = time constant of thermo-potentiostat
@@ -287,8 +287,18 @@ The *fix_modify tf* option enables the Thomas-Fermi metallicity model
    fix_modify ID tf type length voronoi
 
 
-If this option is used parameters must be set for all atom types of the
+If this option is used, these two parameters must be set for
-electrode.
+all atom types of the electrode:
+
+* `tf` is the Thomas-Fermi length :math:`l_{TF}`
+* `voronoi` is the Voronoi volume per atom in units of length cubed
+
+Different types may have different `tf` and `voronoi` values.
+The following self-energy term is then added for all electrode atoms:
+
+.. math::
+
+  A_{ii} += \frac{1}{4 \pi \epsilon_0} \times \frac{4 \pi l_{TF}^2}{\mathrm{Voronoi volume}}
 
 The *fix_modify timer* option turns on (off) additional timer outputs in the log
 file, for code developers to track optimization.
@@ -321,9 +331,11 @@ The global array has *N* rows and *2N+1* columns, where the fix manages
 array, the elements are:
 
 * array[I][1] = total charge that group *I* would have had *if it were
-  at 0 V applied potential* * array[I][2 to *N* + 1] = the *N* entries
+  at 0 V applied potential*
+* array[I][2 to *N* + 1] = the *N* entries
   of the *I*-th row of the electrode capacitance matrix (definition
-  follows) * array[I][*N* + 2 to *2N* + 1] = the *N* entries of the
+  follows)
+* array[I][*N* + 2 to *2N* + 1] = the *N* entries of the
   *I*-th row of the electrode elastance matrix (the inverse of the
   electrode capacitance matrix)
 

doc/src/fix_heat_flow.rst

@@ -1,7 +1,7 @@
 .. index:: fix heat/flow
 
 fix heat/flow command
-==========================
+=====================
 
 Syntax
 """"""
@@ -56,13 +56,19 @@ not invoked during :doc:`energy minimization <minimize>`.
 Restrictions
 """"""""""""
 
+This pair style is part of the GRANULAR package.  It is
+only enabled if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` page for more info.
+
 This fix requires that atoms store temperature and heat flow
 as defined by the :doc:`fix property/atom <fix_property_atom>` command.
 
 Related commands
 """"""""""""""""
 
-:doc:`pair granular <pair_granular>`, :doc:`fix property/atom <fix_property_atom>`
+:doc:`pair granular <pair_granular>`,
+:doc:`fix add/heat <fix_add_heat>`,
+:doc:`fix property/atom <fix_property_atom>`
 
 Default
 """""""

doc/src/fix_indent.rst

@@ -68,10 +68,10 @@ material or as an obstacle in a flow.  Alternatively, it can be used as a
 constraining wall around a simulation; see the discussion of the
 *side* keyword below.
 
-The *gstyle* geometry of the indenter can either be a sphere, a
+The *gstyle* keyword selects the geometry of the indenter and it can
-cylinder, a cone, or a plane.
+either have the value of *sphere*, *cylinder*, *cone*, or *plane*\ .
 
-A spherical indenter exerts a force of magnitude
+A spherical indenter (*gstyle* = *sphere*) exerts a force of magnitude
 
 .. math::
 
@@ -82,13 +82,16 @@ distance from the atom to the center of the indenter, and *R* is the
 radius of the indenter.  The force is repulsive and F(r) = 0 for *r* >
 *R*\ .
 
-A cylindrical indenter exerts the same force, except that *r* is the
+A cylindrical indenter (*gstyle* = *cylinder*) follows the same formula
-distance from the atom to the center axis of the cylinder.  The
+for the force as a sphere, except that *r* is defined the distance
-cylinder extends infinitely along its axis.
+from the atom to the center axis of the cylinder.  The cylinder extends
+infinitely along its axis.
 
-A conical indenter is similar to a cylindrical indenter except that it
+.. versionadded:: 17April2024
-has a finite length (between *lo* and *hi*), and that two different
+
-radii (one at each end, *radlo* and *radhi*) can be defined.
+A conical indenter (*gstyle* = *cone*) is similar to a cylindrical indenter
+except that it has a finite length (between *lo* and *hi*), and that two
+different radii (one at each end, *radlo* and *radhi*) can be defined.
 
 Spherical, cylindrical, and conical indenters account for periodic
 boundaries in two ways.  First, the center point of a spherical
@@ -101,15 +104,15 @@ or axis accounts for periodic boundaries.  Both of these mean that an
 indenter can effectively move through and straddle one or more
 periodic boundaries.
 
-A planar indenter is really an axis-aligned infinite-extent wall
+A planar indenter (*gstyle* = *plane*) behaves like an axis-aligned
-exerting the same force on atoms in the system, where *R* is the
+infinite-extent wall with the same force expression on atoms in the
-position of the plane and *r-R* is the distance from the plane.  If
+system as before, but where *R* is the position of the plane and *r-R*
-the *side* parameter of the plane is specified as *lo* then it will
+is the distance of an from the plane.  If the *side* parameter of the
-indent from the lo end of the simulation box, meaning that atoms with
+plane is specified as *lo* then it will indent from the lo end of the
-a coordinate less than the plane's current position will be pushed
+simulation box, meaning that atoms with a coordinate less than the
-towards the hi end of the box and atoms with a coordinate higher than
+plane's current position will be pushed towards the hi end of the box
-the plane's current position will feel no force.  Vice versa if *side*
+and atoms with a coordinate higher than the plane's current position
-is specified as *hi*\ .
+will feel no force.  Vice versa if *side* is specified as *hi*\ .
 
 Any of the 4 quantities defining a spherical indenter's geometry can
 be specified as an equal-style :doc:`variable <variable>`, namely *x*,

doc/src/fix_ipi.rst

@@ -80,7 +80,7 @@ Obtaining i-PI
 """"""""""""""
 
 Here are the commands to set up a virtual environment and install
-i-PI into it with all its dependencies via the PyPi repository and
+i-PI into it with all its dependencies via the PyPI repository and
 the pip package manager.
 
 .. code-block:: sh

doc/src/fix_pimd.rst

@@ -236,7 +236,7 @@ The keyword *fixcom* specifies whether the center-of-mass of the extended ring-p
 Once *fixcom* is set to be *yes*, the center-of-mass velocity will be distracted from the centroid-mode velocities in each step.
 
 The keyword *lj* should be used if :doc:`lj units <units>` is used for *fix pimd/langevin*. Typically one may want to use
-reduced units to run the simulation, and then convert the results into some physical units (for example, :doc:`metal units <units>`). In this case, the 5 quantities in the physical mass units are needed: epsilon (energy scale), sigma (length scale), mass, Planck's constant, mvv2e (mass * velocity^2 to energy conversion factor). Planck's constant and mvv2e can be found in src/update.cpp. If there is no need to convert reduced units to physical units, set all these five value to 1.
+reduced units to run the simulation, and then convert the results into some physical units (for example, :doc:`metal units <units>`). In this case, the 5 quantities in the physical mass units are needed: epsilon (energy scale), sigma (length scale), mass, Planck's constant, mvv2e (mass * velocity^2 to energy conversion factor). Planck's constant and mvv2e can be found in src/update.cpp. If there is no need to convert reduced units to physical units, you can omit the keyword *lj* and these five values will be set to 1.
 
 The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme
 as described in :ref:`Calhoun <Calhoun>`.  In LAMMPS this is done by using

doc/src/fix_rheo.rst

@@ -0,0 +1,180 @@
+.. index:: fix rheo
+
+fix rheo command
+================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID rheo cut kstyle zmin keyword values...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* rheo = style name of this fix command
+* cut = cutoff for the kernel (distance)
+* kstyle = *quintic* or *RK0* or *RK1* or *RK2*
+* zmin = minimal number of neighbors for reproducing kernels
+* zero or more keyword/value pairs may be appended to args
+* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or
+            *shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
+
+  .. parsed-literal::
+
+       *thermal* values = none, turns on thermal evolution
+       *interface/reconstruct* values = none, reconstructs interfaces with solid particles
+       *surface/detection* values = *sdstyle* *limit* *limit/splash*
+         *sdstyle* = *coordination* or *divergence*
+         *limit* = threshold for surface particles
+         *limit/splash* = threshold for splash particles
+       *shift* values = none, turns on velocity shifting
+       *rho/sum* values = none, uses the kernel to compute the density of particles
+       *self/mass* values = none, a particle uses its own mass in a rho summation
+       *density* values = *rho01*, ... *rho0N* (density)
+       *speed/sound* values = *cs0*, ... *csN* (velocity)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all rheo 3.0 quintic 0 thermal density 0.1 0.1 speed/sound 10.0 1.0
+   fix 1 all rheo 3.0 RK1 10 shift surface/detection coordination 40
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Perform time integration for RHEO particles, updating positions, velocities,
+and densities. For a detailed breakdown of the integration timestep and
+numerical details, see :ref:`(Palermo) <rheo_palermo>`. For an
+overview of other features available in the RHEO package, see
+:doc:`the RHEO howto <Howto_rheo>`.
+
+The type of kernel is specified using *kstyle* and the cutoff is *cut*. Four
+kernels are currently available. The *quintic* kernel is a standard quintic
+spline function commonly used in SPH. The other options, *RK0*, *RK1*, and
+*RK2*, are zeroth, first, and second order reproducing. To generate a
+reproducing kernel, a particle must have sufficient neighbors inside the
+kernel cutoff distance (a coordination number) to accurately calculate
+moments. This threshold is set by *zmin*. If reproducing kernels are
+requested but a particle has fewer neighbors, then it will revert to a
+non-reproducing quintic kernel until it gains more neighbors.
+
+To model temperature evolution, one must specify the *thermal* keyword,
+define a separate instance of :doc:`fix rheo/thermal <fix_rheo_thermal>`,
+and use atom style rheo/thermal.
+
+By default, the density of solid RHEO particles does not evolve and forces
+with fluid particles are calculated using the current velocity of the solid
+particle. If the *interface/reconstruct* keyword is used, then the density
+and velocity of solid particles are alternatively reconstructed for every
+fluid-solid interaction to ensure no-slip and pressure-balanced boundaries.
+This is done by estimating the location of the fluid-solid interface and
+extrapolating fluid particle properties across the interface to calculate a
+temporary apparent density and velocity for a solid particle. The numerical
+details are the same as those described in
+:ref:`(Palermo) <howto_rheo_palermo>` except there is an additional
+restriction that the reconstructed solid density cannot be less than the
+equilibrium density. This prevents fluid particles from sticking to solid
+surfaces.
+
+A modified form of Fickian particle shifting can be enabled with the
+*shift* keyword. This effectively shifts particle positions to generate a
+more uniform spatial distribution. Shifting currently does not consider the
+type of a particle and therefore may be inappropriate in systems consisting
+of multiple fluid phases.
+
+In systems with free surfaces, the *surface/detection* keyword can be used
+to classify the location of particles as being within the bulk fluid, on a
+free surface, or isolated from other particles in a splash or droplet.
+Shifting is then disabled in the normal direction away from the free surface
+to prevent particles from diffusing away. Surface detection can also be used
+to control surface-nucleated effects like oxidation when used in combination
+with :doc:`fix rheo/oxidation <fix_rheo_oxidation>`. Surface detection is not
+performed on solid bodies.
+
+The *surface/detection* keyword takes three arguments: *sdstyle*, *limit*,
+and *limit/splash*. The first, *sdstyle*, specifies whether surface particles
+are identified using a coordination number (*coordination*) or the divergence
+of the local particle positions (*divergence*). The threshold value for a
+surface particle for either of these criteria is set by the numerical value
+of *limit*. Additionally, if a particle's coordination number is too low,
+i.e. if it has separated off from the bulk in a droplet, it is not possible
+to define surfaces and the particle is classified as a splash. The coordination
+threshold for this classification is set by the numerical value of
+*limit/splash*.
+
+By default, RHEO integrates particles' densities using a mass diffusion
+equation. Alternatively, one can update densities every timestep by performing
+a kernel summation of the masses of neighboring particles by specifying the *rho/sum*
+keyword.
+
+The *self/mass* keyword modifies the behavior of the density summation in *rho/sum*.
+Typically, the density :math:`\rho` of a particle is calculated as the sum over neighbors
+
+.. math::
+   \rho_i = \sum_{j} W_{ij} M_j
+
+where :math:`W_{ij}` is the kernel, and :math:`M_j` is the mass of particle :math:`j`.
+The *self/mass* keyword augments this expression by replacing :math:`M_j` with
+:math:`M_i`. This may be useful in simulations of multiple fluid phases with large
+differences in density, :ref:`(Hu) <fix_rheo_hu>`.
+
+The *density* keyword is used to specify the equilibrium density of each of the N
+particle types. It must be followed by N numerical values specifying each type's
+equilibrium density *rho0*.
+
+The *speed/sound* keyword is used to specify the speed of sound of each of the
+N particle types. It must be followed by N numerical values specifying each type's
+speed of sound *cs*.
+
+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.  No global or per-atom quantities are stored
+by this fix for access 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 must be used with atom style rheo or rheo/thermal. This fix must
+be used in conjunction with :doc:`fix rheo/pressure <fix_rheo_pressure>`.
+and :doc:`fix rheo/viscosity <fix_rheo_viscosity>`. If the *thermal* setting
+is used, there must also be an instance of
+:doc:`fix rheo/thermal <fix_rheo_thermal>`. The fix group must be set to all.
+Only one instance of fix rheo may be defined and it  must be defined prior
+to all other RHEO fixes in the input script.
+
+This fix is part of the RHEO 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 rheo/viscosity <fix_rheo_viscosity>`,
+:doc:`fix rheo/pressure <fix_rheo_pressure>`,
+:doc:`fix rheo/thermal <fix_rheo_thermal>`,
+:doc:`pair rheo <pair_rheo>`,
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
+
+Default
+"""""""
+
+*rho0* and *cs* are set to 1.0 for all atom types.
+
+----------
+
+.. _rheo_palermo:
+
+**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.
+
+.. _fix_rheo_hu:
+
+**(Hu)** Hu, and Adams J. Comp. Physics, 213, 844-861 (2006).

doc/src/fix_rheo_oxidation.rst

@@ -0,0 +1,85 @@
+.. index:: fix rheo/oxidation
+
+fix rheo/oxidation command
+==========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID rheo/oxidation cut btype rsurf
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* rheo/oxidation = style name of this fix command
+* cut = maximum bond length (distance units)
+* btype = type of bonds created
+* rsurf = distance from surface to create bonds (distance units)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all rheo/oxidation 1.5 2 0.0
+   fix 1 all rheo/oxidation 1.0 1 2.0
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+This fix dynamically creates bonds on the surface of fluids to
+represent physical processes such as oxidation. It is intended
+for use with bond style :doc:`bond rheo/shell <bond_rheo_shell>`.
+
+Every timestep, particles check neighbors within a distance of *cut*.
+This distance must be smaller than the kernel length defined in
+:doc:`fix rheo <fix_rheo>`. Bonds of type *btype* are created between
+a fluid particle and either a fluid or solid neighbor. The fluid particles
+must also be on the fluid surface, or within a distance of *rsurf* from
+the surface. This process is further described in
+:ref:`(Clemmer) <howto_rheo_clemmer2>`.
+
+If used in conjunction with solid bodies, such as those generated
+by the *react* option of :doc:`fix rheo/thermal <fix_rheo_thermal>`,
+it is recommended to use a :doc:`hybrid bond style <bond_hybrid>`
+with different bond types for solid and oxide bonds.
+
+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.  No global or per-atom quantities are stored
+by this fix for access 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 must be used with the bond style :doc:`rheo/shell <bond_rheo_shell>`
+and :doc:`fix rheo <fix_rheo>` with surface detection enabled.
+
+This fix is part of the RHEO 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 rheo <fix_rheo>`,
+:doc:`bond rheo/shell <bond_rheo_shell>`,
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _howto_rheo_clemmer2:
+
+**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

doc/src/fix_rheo_pressure.rst

@@ -0,0 +1,106 @@
+.. index:: fix rheo/pressure
+
+fix rheo/pressure command
+=========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID rheo/pressure type1 pstyle1 args1 ... typeN pstyleN argsN
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* rheo/pressure = style name of this fix command
+* one or more types and pressure styles must be appended
+* types = lists of types (see below)
+* pstyle = *linear* or *taitwater* or *cubic*
+
+  .. parsed-literal::
+
+       *linear* args = none
+       *taitwater* args = none
+       *cubic* args = cubic prefactor :math:`A_3` (pressure/density\^2)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all rheo/pressure * linear
+   fix 1 all rheo/pressure 1 linear 2 cubic 10.0
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+This fix defines a pressure equation of state for RHEO particles. One can
+define different equations of state for different atom types. An equation
+must be specified for every atom type.
+
+One first defines the atom *types*. A wild-card asterisk can be used in place
+of or in conjunction with the *types* argument to set the coefficients for
+multiple pairs of atom types.  This takes the form "\*" or "\*n" or "m\*"
+or "m\*n".  If :math:`N` is the number of atom types, then an asterisk with
+no numeric values means all types from 1 to :math:`N`.  A leading asterisk
+means all types from 1 to n (inclusive).  A trailing asterisk means all types
+from m to :math:`N` (inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+The *types* definition is followed by the pressure style, *pstyle*. Current
+options *linear*, *taitwater*, and *cubic*. Style *linear* is a linear
+equation of state with a particle pressure :math:`P` calculated as
+
+.. math::
+
+   P = c (\rho - \rho_0)
+
+where :math:`c` is the speed of sound, :math:`\rho_0` is the equilibrium density,
+and :math:`\rho` is the current density of a particle. The numerical values of
+:math:`c` and :math:`\rho_0` are set in :doc:`fix rheo <fix_rheo>`. Style *cubic*
+is a cubic equation of state which has an extra argument :math:`A_3`,
+
+.. math::
+
+   P = c ((\rho - \rho_0) + A_3 (\rho - \rho_0)^3) .
+
+Style *taitwater* is Tait's equation of state:
+
+.. math::
+
+   P = \frac{c^2 \rho_0}{7} \biggl[\left(\frac{\rho}{\rho_0}\right)^{7} - 1\biggr].
+
+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.  No global or per-atom quantities are stored
+by this fix for access 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 must be used with an atom style that includes density
+such as atom_style rheo or rheo/thermal. This fix must be used in
+conjunction with :doc:`fix rheo <fix_rheo>`. The fix group must be
+set to all. Only one instance of fix rheo/pressure can be defined.
+
+This fix is part of the RHEO 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 rheo <fix_rheo>`,
+:doc:`pair rheo <pair_rheo>`,
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
+
+Default
+"""""""
+
+none

doc/src/fix_rheo_thermal.rst

@@ -0,0 +1,128 @@
+.. index:: fix rheo/thermal
+
+fix rheo/thermal command
+========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID rheo/thermal attribute values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* rheo/thermal = style name of this fix command
+* one or more attributes may be appended
+* attribute = *conductivity* or *specific/heat* or *latent/heat* or *Tfreeze* or *react*
+
+  .. parsed-literal::
+
+       *conductivity* args = types style args
+         types = lists of types (see below)
+         style = *constant*
+           *constant* arg = conductivity (power/temperature)
+       *specific/heat* args = types style args
+         types = lists of types (see below)
+         style = *constant*
+           *constant* arg = specific heat (energy/(mass*temperature))
+       *latent/heat* args = types style args
+         types = lists of types (see below)
+         style = *constant*
+           *constant* arg = latent heat (energy/mass)
+       *Tfreeze* args = types style args
+         types = lists of types (see below)
+         style = *constant*
+           *constant* arg = freezing temperature (temperature)
+       *react* args = cut type
+         cut = maximum bond distance
+         type = bond type
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all rheo/thermal conductivity * constant 1.0 specific/heat * constant 1.0 Tfreeze * constant 1.0
+   fix 1 all rheo/pressure conductivity 1*2 constant 1.0 conductivity 3*4 constant 2.0 specific/heat * constant 1.0
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+This fix performs time integration of temperature for atom style rheo/thermal.
+In addition, it defines multiple thermal properties of particles and handles
+melting/solidification, if applicable. For more details on phase transitions
+in RHEO, see :doc:`the RHEO howto <Howto_rheo>`.
+
+Note that the temperature of a particle is always derived from the energy.
+This implies the *temperature* attribute of :doc:`the set command <set>` does
+not affect particles. Instead, one should use the *sph/e* attribute.
+
+For each atom type, one can define expressions for the *conductivity*,
+*specific/heat*, *latent/heat*, and critical temperature (*Tfreeze*).
+The conductivity and specific heat must be defined for all atom types.
+The latent heat and critical temperature are optional. However, a
+critical temperature must be defined to specify a latent heat.
+
+Note, if shifting is turned on in :doc:`fix rheo <fix_rheo>`, the gradient
+of the energy is used to shift energies. This may be inappropriate in systems
+with multiple atom types with different specific heats.
+
+For each property, one must first define a list of atom types. A wild-card
+asterisk can be used in place of or in conjunction with the *types* argument
+to set the coefficients for multiple pairs of atom types.  This takes the
+form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N` is the number of atom
+types, then an asterisk with no numeric values means all types from 1 to
+:math:`N`.  A leading asterisk means all types from 1 to n (inclusive).
+A trailing asterisk means all types from m to :math:`N` (inclusive).  A
+middle asterisk means all types from m to n (inclusive).
+
+The *types* definition for each property is followed by the style. Currently,
+the only option is *constant*. Style *constant* simply applies a constant value
+of respective property to each particle of the assigned type.
+
+The *react* keyword controls whether bonds are created/deleted when particles
+transition between a fluid and solid state. This option only applies to atom
+types that have a defined value of *Tfreeze*. When a fluid particle's
+temperature drops below *Tfreeze*, bonds of type *btype* are created between
+nearby solid particles within a distance of *cut*. The particle's status also
+swaps to a solid state. When a solid particle's temperature rises above
+*Tfreeze*, all bonds of type *btype* are broken and the particle's status swaps
+to a fluid state.
+
+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.  No global or per-atom quantities are stored
+by this fix for access 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 must be used with an atom style that includes temperature,
+heatflow, and conductivity such as atom_style rheo/thermal This fix
+must be used in conjunction with :doc:`fix rheo <fix_rheo>` with the
+*thermal* setting. The fix group must be set to all. Only one
+instance of fix rheo/pressure can be defined.
+
+This fix is part of the RHEO 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 rheo <fix_rheo>`,
+:doc:`pair rheo <pair_rheo>`,
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`,
+:doc:`fix add/heat <fix_add_heat>`
+
+Default
+"""""""
+
+none

doc/src/fix_rheo_viscosity.rst

@@ -0,0 +1,117 @@
+.. index:: fix rheo/viscosity
+
+fix rheo/viscosity command
+==========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID rheo/viscosity type1 pstyle1 args1 ... typeN pstyleN argsN
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* rheo/viscosity = style name of this fix command
+* one or more types and viscosity styles must be appended
+* types = lists of types (see below)
+* vstyle = *constant* or *power*
+
+  .. parsed-literal::
+
+       *constant* args = *eta*
+         *eta* = viscosity
+
+       *power* args = *eta*, *gd0*, *K*, *n*
+         *eta* = viscosity
+         *gd0* = critical strain rate
+         *K* = consistency index
+         *n* = power-law exponent
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all rheo/viscosity * constant 1.0
+   fix 1 all rheo/viscosity 1 constant 1.0 2 power 0.1 5e-4 0.001 0.5
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+This fix defines a viscosity for RHEO particles. One can define different
+viscosities for different atom types, but a viscosity must be specified for
+every atom type.
+
+One first defines the atom *types*. A wild-card asterisk can be used in place
+of or in conjunction with the *types* argument to set the coefficients for
+multiple pairs of atom types.  This takes the form "\*" or "\*n" or "m\*"
+or "m\*n".  If :math:`N` is the number of atom types, then an asterisk with
+no numeric values means all types from 1 to :math:`N`.  A leading asterisk
+means all types from 1 to n (inclusive).  A trailing asterisk means all types
+from m to :math:`N` (inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+The *types* definition is followed by the viscosity style, *vstyle*. Two
+options are available, *constant* and *power*. Style *constant* simply
+applies a constant value of the viscosity *eta* to each particle of the
+assigned type. Style *power* is a Hershchel-Bulkley constitutive equation
+for the stress :math:`\tau`
+
+.. math::
+
+   \tau = \left(\frac{\tau_0}{\dot{\gamma}} + K \dot{\gamma}^{n - 1}\right) \dot{\gamma}, \tau \ge \tau_0
+
+where :math:`\dot{\gamma}` is the strain rate and :math:`\tau_0` is the critical
+yield stress, below which :math:`\dot{\gamma} = 0.0`. To avoid divergences, this
+expression is regularized by defining a critical strain rate *gd0*. If the local
+strain rate on a particle falls below this limit, a constant viscosity of *eta*
+is assigned. This implies a value of
+
+.. math::
+   \tau_0 = \eta \dot{\gamma}_0 - K \dot{\gamma}_0^N
+
+as further discussed in :ref:`(Palermo) <rheo_palermo2>`.
+
+
+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.  No global or per-atom quantities are stored
+by this fix for access 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 must be used with an atom style that includes viscosity
+such as atom_style rheo or rheo/thermal. This fix must be used in
+conjunction with :doc:`fix rheo <fix_rheo>`. The fix group must be
+set to all. Only one instance of fix rheo/viscosity can be defined.
+
+This fix is part of the RHEO 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 rheo <fix_rheo>`,
+:doc:`pair rheo <pair_rheo>`,
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _rheo_palermo2:
+
+**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.

doc/src/fix_store_force.rst

@@ -23,11 +23,12 @@ Examples
 Description
 """""""""""
 
-Store the forces on atoms in the group at the point during each
+Store the forces on atoms in the group at the point during each timestep
-timestep when the fix is invoked, as described below.  This is useful
+when the fix is invoked, as described below.  This is useful for storing
-for storing forces before constraints or other boundary conditions are
+forces before constraints or other boundary conditions are computed
-computed which modify the forces, so that unmodified forces can be
+which modify the forces, so that unmodified forces can be :doc:`written
-:doc:`written to a dump file <dump>` or accessed by other :doc:`output commands <Howto_output>` that use per-atom quantities.
+to a dump file <dump>` or accessed by other :doc:`output commands
+<Howto_output>` that use per-atom quantities.
 
 This fix is invoked at the point in the velocity-Verlet timestepping
 immediately after :doc:`pair <pair_style>`, :doc:`bond <bond_style>`,
@@ -36,12 +37,13 @@ immediately after :doc:`pair <pair_style>`, :doc:`bond <bond_style>`,
 forces have been calculated.  It is the point in the timestep when
 various fixes that compute constraint forces are calculated and
 potentially modify the force on each atom.  Examples of such fixes are
-:doc:`fix shake <fix_shake>`, :doc:`fix wall <fix_wall>`, and :doc:`fix indent <fix_indent>`.
+:doc:`fix shake <fix_shake>`, :doc:`fix wall <fix_wall>`, and :doc:`fix
+indent <fix_indent>`.
 
 .. note::
 
-   The order in which various fixes are applied which operate at
+   The order in which various fixes are applied which operate at the
-   the same point during the timestep, is the same as the order they are
+   same point during the timestep, is the same as the order they are
    specified in the input script.  Thus normally, if you want to store
    per-atom forces due to force field interactions, before constraints
    are applied, you should list this fix first within that set of fixes,
@@ -52,8 +54,9 @@ potentially modify the force on each atom.  Examples of such fixes are
 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
+No information about this fix is written to :doc:`binary restart files
-are relevant to this fix.
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
+relevant to this fix.
 
 This fix produces a per-atom array which can be accessed by various
 :doc:`output commands <Howto_output>`.  The number of columns for each
@@ -61,7 +64,8 @@ atom is 3, and the columns store the x,y,z forces on each atom.  The
 per-atom values be accessed on any timestep.
 
 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/labelmap.rst

@@ -44,8 +44,8 @@ The label map can also be defined by the :doc:`read_data <read_data>`
 command when it reads these sections in a data file: Atom Type Labels,
 Bond Type Labels, etc.  See the :doc:`Howto type labels
 <Howto_type_labels>` doc page for a general discussion of how type
-labels can be used.  See :ref:`(Gissinger) <Typelabel>` for a discussion
+labels can be used.  See :ref:`(Gissinger) <Typelabel1>` for a
-of the type label implementation in LAMMPS and its uses.
+discussion of the type label implementation in LAMMPS and its uses.
 
 Valid type labels can contain any alphanumeric character, but must not
 start with a number, a '#', or a '*' character.  They can contain other
@@ -103,6 +103,6 @@ none
 
 -----------
 
-.. _Typelabel:
+.. _Typelabel1:
 
 **(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).

doc/src/pair_charmm.rst

@@ -112,26 +112,22 @@ Description
 These pair styles compute Lennard Jones (LJ) and Coulombic
 interactions with additional switching or shifting functions that ramp
 the energy and/or force smoothly to zero between an inner and outer
-cutoff.  They are implementations of the widely used CHARMM force
+cutoff.  They implement the widely used CHARMM force field, see
-field used in the `CHARMM <https://www.charmm.org>`_ MD code (and
+:doc:`Howto discussion on biomolecular force fields <Howto_bioFF>` for
-others).  See :ref:`(MacKerell) <pair-MacKerell>` for a description of the
+details.
-CHARMM force field.
 
 The styles with *charmm* (not *charmmfsw* or *charmmfsh*\ ) in their
 name are the older, original LAMMPS implementations.  They compute the
-LJ and Coulombic interactions with an energy switching function (esw,
+LJ and Coulombic interactions with an energy switching function which
-shown in the formula below as S(r)), which ramps the energy smoothly
+ramps the energy smoothly to zero between the inner and outer cutoff.
-to zero between the inner and outer cutoff.  This can cause
+This can cause irregularities in pairwise forces (due to the discontinuous
-irregularities in pairwise forces (due to the discontinuous second
+second derivative of energy at the boundaries of the switching region),
-derivative of energy at the boundaries of the switching region), which
+which in some cases can result in detectable artifacts in an MD simulation.
-in some cases can result in detectable artifacts in an MD simulation.
 
 The newer styles with *charmmfsw* or *charmmfsh* in their name replace
 the energy switching with force switching (fsw) and force shifting
 (fsh) functions, for LJ and Coulombic interactions respectively.
-These follow the formulas and description given in
+
-:ref:`(Steinbach) <Steinbach>` and :ref:`(Brooks) <Brooks1>` to minimize these
-artifacts.
 
 .. note::
 
@@ -152,26 +148,6 @@ artifacts.
    the CHARMM force field energies and forces, when using one of these
    two CHARMM pair styles.
 
-.. math::
-
-   E = & LJ(r) \qquad \qquad \qquad r < r_{\rm in} \\
-     = & S(r) * LJ(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
-     = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
-   E = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\
-     = & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
-     = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
-   LJ(r) = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
-           \left(\frac{\sigma}{r}\right)^6 \right] \\
-   C(r) = & \frac{C q_i q_j}{ \epsilon r} \\
-   S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2
-     \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]}
-   { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
-
-where S(r) is the energy switching function mentioned above for the
-*charmm* styles.  See the :ref:`(Steinbach) <Steinbach>` paper for the
-functional forms of the force switching and force shifting functions
-used in the *charmmfsw* and *charmmfsh* styles.
-
 When using the *lj/charmm/coul/charmm styles*, both the LJ and
 Coulombic terms require an inner and outer cutoff. They can be the
 same for both formulas or different depending on whether 2 or 4

doc/src/pair_coul.rst

@@ -2,6 +2,8 @@
 .. index:: pair_style coul/cut/gpu
 .. index:: pair_style coul/cut/kk
 .. index:: pair_style coul/cut/omp
+.. index:: pair_style coul/cut/global
+.. index:: pair_style coul/cut/global/omp
 .. index:: pair_style coul/debye
 .. index:: pair_style coul/debye/gpu
 .. index:: pair_style coul/debye/kk
@@ -11,8 +13,6 @@
 .. index:: pair_style coul/dsf/kk
 .. index:: pair_style coul/dsf/omp
 .. index:: pair_style coul/exclude
-.. index:: pair_style coul/cut/global
-.. index:: pair_style coul/cut/global/omp
 .. index:: pair_style coul/long
 .. index:: pair_style coul/long/omp
 .. index:: pair_style coul/long/kk
@@ -33,6 +33,11 @@ pair_style coul/cut command
 
 Accelerator Variants: *coul/cut/gpu*, *coul/cut/kk*, *coul/cut/omp*
 
+pair_style coul/cut/global command
+==================================
+
+Accelerator Variants: *coul/cut/omp*
+
 pair_style coul/debye command
 =============================
 
@@ -46,11 +51,6 @@ Accelerator Variants: *coul/dsf/gpu*, *coul/dsf/kk*, *coul/dsf/omp*
 pair_style coul/exclude command
 ===============================
 
-pair_style coul/cut/global command
-==================================
-
-Accelerator Variants: *coul/cut/omp*
-
 pair_style coul/long command
 ============================
 
@@ -79,16 +79,17 @@ pair_style tip4p/long command
 
 Accelerator Variants: *tip4p/long/omp*
 
+
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
    pair_style coul/cut cutoff
+   pair_style coul/cut/global cutoff
    pair_style coul/debye kappa cutoff
    pair_style coul/dsf alpha cutoff
    pair_style coul/exclude cutoff
-   pair_style coul/cut/global cutoff
    pair_style coul/long cutoff
    pair_style coul/wolf alpha cutoff
    pair_style coul/streitz cutoff keyword alpha
@@ -152,6 +153,11 @@ the 2 atoms, and :math:`\epsilon` is the dielectric constant which can be set
 by the :doc:`dielectric <dielectric>` command.  The cutoff :math:`r_c` truncates
 the interaction distance.
 
+Pair style *coul/cut/global* computes the same Coulombic interactions
+as style *coul/cut* except that it allows only a single global cutoff
+and thus makes it compatible for use in combination with long-range
+coulomb styles in :doc:`hybrid pair styles <pair_hybrid>`.
+
 ----------
 
 Style *coul/debye* adds an additional exp() damping factor to the
@@ -262,11 +268,6 @@ Streitz-Mintmire parameterization for the material being modeled.
 
 ----------
 
-Pair style *coul/cut/global* computes the same Coulombic interactions
-as style *coul/cut* except that it allows only a single global cutoff
-and thus makes it compatible for use in combination with long-range
-coulomb styles in :doc:`hybrid pair styles <pair_hybrid>`.
-
 Pair style *coul/exclude* computes Coulombic interactions like *coul/cut*
 but **only** applies them to excluded pairs using a scaling factor
 of :math:`\gamma - 1.0` with :math:`\gamma` being the factor assigned

doc/src/pair_dpd_coul_slater_long.rst

@@ -13,16 +13,11 @@ Syntax
 
    pair_style dpd/coul/slater/long T cutoff_DPD seed lambda cutoff_coul
 
-   pair_coeff I J a_IJ Gamma is_charged
+* T = temperature (temperature units)
-
-* T = temperature (temperature units) (dpd only)
 * cutoff_DPD = global cutoff for DPD interactions (distance units)
 * seed = random # seed (positive integer)
 * lambda = decay length of the charge (distance units)
-* cutoff_coul = real part cutoff for Coulombic interactions (distance units)
+* cutoff_coul = global cutoff for Coulombic interactions (distance units)
-* I,J = numeric atom types, or type labels
-* Gamma = DPD Gamma coefficient
-* is_charged (boolean) set to yes if I and J are charged beads
 
 Examples
 """"""""
@@ -30,6 +25,7 @@ Examples
 .. code-block:: LAMMPS
 
    pair_style dpd/coul/slater/long 1.0 2.5 34387 0.25 3.0
+
    pair_coeff 1 1 78.0 4.5          # not charged by default
    pair_coeff 2 2 78.0 4.5 yes
 
@@ -37,59 +33,82 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 27June2024
 
-Style *dpd/coul/slater/long* computes a force field for dissipative particle dynamics
+Style *dpd/coul/slater/long* computes a force field for dissipative
-(DPD) following the exposition in :ref:`(Groot) <Groot5>` with the addition of
+particle dynamics (DPD) following the exposition in :ref:`(Groot)
-electrostatic interactions. The coulombic forces in mesoscopic models
+<Groot5>`.  It also allows for the use of charged particles in the
-employ potentials without explicit excluded-volume interactions.
+model by adding a long-range Coulombic term to the DPD interactions.
-The goal is to prevent artificial ionic pair formation by including a charge
+The short-range portion of the Coulombics is calculated by this pair
-distribution in the Coulomb potential, following the formulation of
+style.  The long-range Coulombics are computed by use of the
-:ref:`(Melchor) <Melchor1>`:
+:doc:`kspace_style <kspace_style>` command, e.g. using the Ewald or
+PPPM styles.
 
-The force on bead I due to bead J is given as a sum
+Coulombic forces in mesoscopic models such as DPD employ potentials
-of 4 terms
+without explicit excluded-volume interactions.  The goal is to prevent
+artificial ionic pair formation by including a charge distribution in
+the Coulomb potential, following the formulation in :ref:`(Melchor1)
+<Melchor1>`.
+
+.. note::
+
+   This pair style is effectively the combination of the
+   :doc:`pair_style dpd <pair_dpd>` and :doc:`pair_style
+   coul/slater/long <pair_coul_slater>` commands, but should be more
+   efficient (especially on GPUs) than using :doc:`pair_style
+   hybrid/overlay dpd coul/slater/long <pair_hybrid>`. That is
+   particularly true for the GPU package version of the pair style since
+   this version is compatible with computing neighbor lists on the GPU
+   instead of the CPU as is required for hybrid styles.
+
+In the charged DPD model, the force on bead I due to bead J is given
+as a sum of 4 terms:
 
 .. math::
 
    \vec{f}  = & (F^C + F^D + F^R + F^E) \hat{r_{ij}} \\
-   F^C      = & A w(r) \qquad \qquad \qquad \qquad \qquad r < r_c \\
+   F^C      = & A w(r) \qquad \qquad \qquad \qquad \qquad r < r_{DPD} \\
-   F^D      = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v}_{ij}) \qquad \qquad r < r_c \\
+   F^D      = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v}_{ij}) \qquad \qquad r < r_{DPD} \\
-   F^R      = & \sigma w(r) \alpha (\Delta t)^{-1/2} \qquad \qquad \qquad r < r_c \\
+   F^R      = & \sigma w(r) \alpha (\Delta t)^{-1/2} \qquad \qquad \qquad r < r_{DPD} \\
-   w(r)     = & 1 - \frac{r}{r_c} \\
+   w(r)     = & 1 - \frac{r}{r_{DPD}} \\
    F^E      = & \frac{C q_iq_j}{\epsilon r^2} \left( 1- exp\left( \frac{2r_{ij}}{\lambda} \right) \left( 1 + \frac{2r_{ij}}{\lambda} \left( 1 + \frac{r_{ij}}{\lambda} \right)\right) \right)
 
-where :math:`F^C` is a conservative force, :math:`F^D` is a dissipative
+where :math:`F^C` is a conservative force, :math:`F^D` is a
-force, :math:`F^R` is a random force, and :math:`F^E` is an electrostatic force.
+dissipative force, :math:`F^R` is a random force, and :math:`F^E` is
-:math:`\hat{r_{ij}}` is a unit vector in the direction
+an electrostatic force.  :math:`\hat{r_{ij}}` is a unit vector in the
-:math:`r_i - r_j`, :math:`\vec{v}_{ij}` is
+direction :math:`r_i - r_j`, :math:`\vec{v}_{ij}` is the vector
-the vector difference in velocities of the two atoms :math:`\vec{v}_i -
+difference in velocities of the two atoms :math:`\vec{v}_i -
 \vec{v}_j`, :math:`\alpha` is a Gaussian random number with zero mean
 and unit variance, *dt* is the timestep size, and :math:`w(r)` is a
-weighting factor that varies between 0 and 1.  :math:`r_c` is the
+weighting factor that varies between 0 and 1.
-pairwise cutoff.  :math:`\sigma` is set equal to :math:`\sqrt{2 k_B T
-\gamma}`, where :math:`k_B` is the Boltzmann constant and *T* is the
-temperature parameter in the pair_style command.
-C is the same Coulomb conversion factor as in the pair_styles
-coul/cut and coul/long. In this way the Coulomb
-interaction between ions is corrected at small distances r, and
-the long-range interactions are computed either by the Ewald or the PPPM technique.
 
+:math:`\sigma` is set equal to :math:`\sqrt{2 k_B T \gamma}`, where
+:math:`k_B` is the Boltzmann constant and *T* is the temperature
+parameter in the pair_style command.
 
-The following parameters must be defined for each
+:math:`r_{DPD}` is the pairwise cutoff for the first 3 DPD terms in
-pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command as in
+the formula as specified by *cutoff_DPD*.  For the :math:`F^E` term,
-the examples above, or in the data file or restart files read by the
+pairwise interactions within the specified *cutoff_coul* distance are
+computed directly; interactions beyond that distance are computed in
+reciprocal space.  *C* is the same Coulomb conversion factor used in
+the Coulombic formulas described on the :doc:`pair_coul <pair_coul>`
+doc page.
+
+The following parameters must be defined for each pair of atoms types
+via the :doc:`pair_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
 :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
 commands:
 
 * A (force units)
 * :math:`\gamma` (force/velocity units)
-* is_charged (boolean)
+* is_charged (optional boolean, default = no)
 
-
+The *is_charged* parameter is optional and can be specified as *yes* or
-.. note::
+*no*.  *Yes* should be used for interactions between two types of
-
+charged particles.  *No* is the default and should be used for
-   This style is the combination of :doc:`pair_style dpd <pair_dpd>` and :doc:`pair_style coul/slater/long <pair_coul_slater>`.
+interactions between two types of particles when one or both are
+uncharged.
 
 ----------
 
@@ -116,17 +135,17 @@ pressure.
 This pair style writes its information to :doc:`binary restart files
 <restart>`, so pair_style and pair_coeff commands do not need to be
 specified in an input script that reads a restart file.  Note that the
-user-specified random number seed is stored in the restart file, so when
+user-specified random number seed is stored in the restart file, so
-a simulation is restarted, each processor will re-initialize its random
+when a simulation is restarted, each processor will re-initialize its
-number generator the same way it did initially.  This means the random
+random number generator the same way it did initially.  This means the
-forces will be random, but will not be the same as they would have been
+random forces will be random, but will not be the same as they would
-if the original simulation had continued past the restart time.
+have been if the original simulation had continued past the restart
+time.
 
 This pair style can only be used via the *pair* keyword of the
-:doc:`run_style respa <run_style>` command.  They do not support the
+:doc:`run_style respa <run_style>` command.  It does not support the
 *inner*, *middle*, *outer* keywords.
 
-
 ----------
 
 Restrictions
@@ -138,17 +157,17 @@ LAMMPS was built with that package.  See the :doc:`Build package
 
 The default frequency for rebuilding neighbor lists is every 10 steps
 (see the :doc:`neigh_modify <neigh_modify>` command). This may be too
-infrequent since particles move rapidly and
+infrequent since particles move rapidly and can overlap by large
-can overlap by large amounts.  If this setting yields a non-zero number
+amounts.  If this setting yields a non-zero number of "dangerous"
-of "dangerous" reneighborings (printed at the end of a simulation), you
+reneighborings (printed at the end of a simulation), you should
-should experiment with forcing reneighboring more often and see if
+experiment with forcing reneighboring more often and see if system
-system energies/trajectories change.
+energies/trajectories change.
 
-This pair style requires you to use the :doc:`comm_modify vel yes
+This pair style requires use of the :doc:`comm_modify vel yes
 <comm_modify>` command so that velocities are stored by ghost atoms.
 
-This pair style also requires the long-range solvers included in the KSPACE package.
+This pair style also requires use of a long-range solvers from the
-
+KSPACE package.
 
 This pair style will not restart exactly when using the
 :doc:`read_restart <read_restart>` command, though they should provide
@@ -160,13 +179,11 @@ Related commands
 """"""""""""""""
 
 :doc:`pair_style dpd <pair_dpd>`, :doc:`pair_style coul/slater/long <pair_coul_slater>`,
-:doc:`pair_coeff <pair_coeff>`, :doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`,
-:doc:`pair_style srp <pair_srp>`, :doc:`fix mvv/dpd <fix_mvv_dpd>`.
 
 Default
 """""""
 
-is_charged = no
+For the pair_coeff command, the default is is_charged = no.
 
 ----------
 

doc/src/pair_pod.rst

@@ -1,8 +1,11 @@
 .. index:: pair_style pod
+.. index:: pair_style pod/kk
 
 pair_style pod command
 ========================
 
+Accelerator Variants: *pod/kk*
+
 Syntax
 """"""
 
@@ -24,29 +27,33 @@ Description
 .. versionadded:: 22Dec2022
 
 Pair style *pod* defines the proper orthogonal descriptor (POD)
-potential :ref:`(Nguyen) <Nguyen20221>`.  The mathematical definition of
+potential :ref:`(Nguyen and Rohskopf) <Nguyen20222b>`,
-the POD potential is described from :doc:`fitpod <fitpod_command>`, which is
+:ref:`(Nguyen2023) <Nguyen20232b>`, :ref:`(Nguyen2024) <Nguyen20242b>`,
-used to fit the POD potential to *ab initio* energy and force data.
+and :ref:`(Nguyen and Sema) <Nguyen20243b>`.  The :doc:`fitpod
+<fitpod_command>` is used to fit the POD potential.
 
 Only a single pair_coeff command is used with the *pod* style which
-specifies a POD parameter file followed by a coefficient file.
+specifies a POD parameter file followed by a coefficient file, a
+projection matrix file, and a centroid file.
 
-The coefficient file (``Ta_coefficients.pod``) contains coefficients for the
+The POD parameter file (``Ta_param.pod``) can contain blank and comment
-POD potential. The top of the coefficient file can contain any number of
+lines (start with #) anywhere. Each non-blank non-comment line must
-blank and comment lines (start with #), but follows a strict format
+contain one keyword/value pair. See :doc:`fitpod <fitpod_command>` for
-after that. The first non-blank non-comment line must contain:
+the description of all the keywords that can be assigned in the
+parameter file.
 
-* POD_coefficients: *ncoeff*
+The coefficient file (``Ta_coefficients.pod``) contains coefficients for
+the POD potential. The top of the coefficient file can contain any
+number of blank and comment lines (start with #), but follows a strict
+format after that. The first non-blank non-comment line must contain:
 
-This is followed by *ncoeff* coefficients, one per line. The coefficient
+* model_coefficients: *ncoeff* *nproj* *ncentroid*
+
+This is followed by *ncoeff* coefficients, *nproj* projection matrix entries,
+and *ncentroid* centroid coordinates, one per line. The coefficient
 file is generated after training the POD potential using :doc:`fitpod
 <fitpod_command>`.
 
-The POD parameter file (``Ta_param.pod``) can contain blank and comment lines
-(start with #) anywhere. Each non-blank non-comment line must contain
-one keyword/value pair. See :doc:`fitpod <fitpod_command>` for the description
-of all the keywords that can be assigned in the parameter file.
-
 As an example, if a LAMMPS indium phosphide simulation has 4 atoms
 types, with the first two being indium and the third and fourth being
 phophorous, the pair_coeff command would look like this:
@@ -67,7 +74,33 @@ the *hybrid* pair style.  The NULL values are placeholders for atom
 types that will be used with other potentials.
 
 Examples about training and using POD potentials are found in the
-directory lammps/examples/PACKAGES/pod.
+directory lammps/examples/PACKAGES/pod and the Github repo https://github.com/cesmix-mit/pod-examples.
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS with
+user-specifiable parameters as described above.  You never need to
+specify a pair_coeff command with I != J arguments for this style.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart
+files <restart>`, since it is stored in potential files.  Thus, you need
+to re-specify the pair_style and pair_coeff commands in an input script
+that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  It does not support the
+*inner*, *middle*, *outer* keywords.
+
+----------
+
+.. include:: accel_styles.rst
 
 ----------
 
@@ -78,12 +111,14 @@ This style is part of the ML-POD package.  It is only enabled if LAMMPS
 was built with that package. See the :doc:`Build package
 <Build_package>` page for more info.
 
-This pair style does not compute per-atom energies and per-atom stresses.
-
 Related commands
 """"""""""""""""
 
 :doc:`fitpod <fitpod_command>`,
+:doc:`compute pod/atom <compute_pod_atom>`,
+:doc:`compute podd/atom <compute_pod_atom>`,
+:doc:`compute pod/local <compute_pod_atom>`,
+:doc:`compute pod/global <compute_pod_atom>`
 
 Default
 """""""
@@ -92,6 +127,20 @@ none
 
 ----------
 
-.. _Nguyen20221:
+.. _Nguyen20222b:
+
+**(Nguyen and Rohskopf)** Nguyen and Rohskopf,  Journal of Computational Physics, 480, 112030, (2023).
+
+.. _Nguyen20232b:
+
+**(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023).
+
+.. _Nguyen20242b:
+
+**(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024).
+
+.. _Nguyen20243b:
+
+**(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
+
 
-**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022).

doc/src/pair_rheo.rst

@@ -0,0 +1,102 @@
+.. index:: pair_style rheo
+
+pair_style rheo command
+=======================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style rheo cutoff keyword values
+
+* cutoff = global cutoff for kernel (distance units)
+* zero or more keyword/value pairs may be appended to args
+* keyword = *rho/damp* or *artificial/visc* or *harmonic/means*
+
+.. parsed-literal::
+
+     *rho/damp* args = density damping prefactor :math:`\xi`
+     *artificial/visc* args = artificial viscosity prefactor :math:`\zeta`
+     *harmonic/means* args = none
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style rheo 3.0 rho/damp 1.0 artificial/visc 2.0
+   pair_coeff * *
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Pair style *rheo* computes pressure and viscous forces between particles
+in the :doc:`rheo package <Howto_rheo>`. If thermal evolution is turned
+on in :doc:`fix rheo <fix_rheo>`, then the pair style also calculates
+heat exchanged between particles.
+
+The *artificial/viscosity* keyword is used to specify the magnitude
+:math:`\zeta` of an optional artificial viscosity contribution to forces.
+This factor can help stabilize simulations by smoothing out small length
+scale variations in velocity fields. Artificial viscous forces typically
+are only exchanged by fluid particles. However, if interfaces are not
+reconstructed in fix rheo, fluid particles will also exchange artificial
+viscous forces with solid particles to improve stability.
+
+The *rho/damp* keyword is used to specify the magnitude :math:`\xi` of
+an optional pairwise damping term between the density of particles. This
+factor can help stabilize simulations by smoothing out small length
+scale variations in density fields. However, in systems that develop
+a density gradient in equilibrium (e.g. in a hydrostatic column underlying
+gravity), this option may be inappropriate.
+
+If particles have different viscosities or conductivities, the
+*harmonic/means* keyword changes how they are averaged before calculating
+pairwise forces or heat exchanges. By default, an arithmetic averaged is
+used, however, a harmonic mean may improve stability in systems with multiple
+fluid phases with large disparities in viscosities.
+
+No coefficients are defined for each pair of atoms types via the
+:doc:`pair_coeff <pair_coeff>` command as in the examples
+above.
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This style does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+This style does not write information to :doc:`binary restart files <restart>`.
+Thus, you need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+This style can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  It does not support the *inner*,
+*middle*, *outer* keywords.
+
+Restrictions
+""""""""""""
+
+This fix is part of the RHEO 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 rheo <fix_rheo>`,
+:doc:`fix rheo/pressure <fix_rheo_pressure>`,
+:doc:`fix rheo/thermal <fix_rheo_thermal>`,
+:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
+
+Default
+"""""""
+
+Density damping and artificial viscous forces are not calculated.
+Arithmetic means are used for mixing particle properties.

doc/src/pair_rheo_solid.rst

@@ -0,0 +1,112 @@
+.. index:: pair_style rheo/solid
+
+pair_style rheo/solid command
+=============================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style rheo/solid
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style rheo/solid
+   pair_coeff * * 1.0 1.5 1.0
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Style *rheo/solid* is effectively a copy of pair style
+:doc:`bpm/spring <pair_bpm_spring>` except it only applies forces
+between solid RHEO particles, determined by checking the status of
+each pair of neighboring particles before calculating forces.
+
+The style computes pairwise forces with the formula
+
+.. math::
+
+   F = k (r - r_c)
+
+where :math:`k` is a stiffness and :math:`r_c` is the cutoff length.
+An additional damping force is also applied to interacting
+particles. The force is proportional to the difference in the
+normal velocity of particles
+
+.. math::
+
+   F_D = - \gamma w (\hat{r} \bullet \vec{v})
+
+where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
+displacement normal vector, :math:`\vec{v}` is the velocity difference
+between the two particles, and :math:`w` is a smoothing factor.
+This smoothing factor is constructed such that damping forces go to zero
+as particles come out of contact to avoid discontinuities. It is
+given by
+
+.. math::
+
+   w = 1.0 - \left( \frac{r}{r_c} \right)^8 .
+
+The following coefficients must be defined for each pair of atom types
+via the :doc:`pair_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
+commands, or by mixing as described below:
+
+* :math:`k`             (force/distance units)
+* :math:`r_c`           (distance units)
+* :math:`\gamma`        (force/velocity units)
+
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+For atom type pairs I,J and I != J, the A coefficient and cutoff
+distance for this pair style can be mixed.  A is always mixed via a
+*geometric* rule.  The cutoff is mixed according to the pair_modify
+mix value.  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 option, since the pair interaction goes to 0.0 at the cutoff.
+
+The :doc:`pair_modify <pair_modify>` table and tail options are not
+relevant for this pair style.
+
+This pair style writes its information to :doc:`binary restart files
+<restart>`, so pair_style and pair_coeff commands do not need to be
+specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  It does not support the
+*inner*, *middle*, *outer* keywords.
+
+----------
+
+Restrictions
+""""""""""""
+
+This pair style is part of the RHEO 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 rheo <fix_rheo>`,
+:doc:`fix rheo/thermal <fix_rheo_thermal>`,
+:doc:`pair bpm/spring <pair_bpm_spring>`
+
+Default
+"""""""
+
+none

doc/src/pair_style.rst

@@ -292,6 +292,7 @@ accelerated styles exist.
 * :doc:`mesocnt/viscous <pair_mesocnt>` - Mesoscopic vdW potential for (carbon) nanotubes with friction
 * :doc:`mgpt <pair_mgpt>` - Simplified model generalized pseudopotential theory (MGPT) potential
 * :doc:`mie/cut <pair_mie>` - Mie potential
+* :doc:`mliap <pair_mliap>` - Multiple styles of machine-learning potential
 * :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - Smoothed MM3 vdW potential with Gaussian electrostatics
 * :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
 * :doc:`morse <pair_morse>` - Morse potential
@@ -337,6 +338,8 @@ accelerated styles exist.
 * :doc:`reaxff <pair_reaxff>` - ReaxFF potential
 * :doc:`rebo <pair_airebo>` - Second generation REBO potential of Brenner
 * :doc:`rebomos <pair_rebomos>` - REBOMoS potential for MoS2
+* :doc:`rheo <pair_rheo>` - fluid interactions in RHEO package
+* :doc:`rheo/solid <pair_rheo_solid>` - solid interactions in RHEO package
 * :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
 * :doc:`saip/metal <pair_saip_metal>` - Interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
 * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - Smoothed dissipative particle dynamics for water at isothermal conditions
@@ -347,7 +350,6 @@ accelerated styles exist.
 * :doc:`smd/tri_surface <pair_smd_triangulated_surface>` -
 * :doc:`smd/ulsph <pair_smd_ulsph>` -
 * :doc:`smtbq <pair_smtbq>` -
-* :doc:`mliap <pair_mliap>` - Multiple styles of machine-learning potential
 * :doc:`snap <pair_snap>` - SNAP machine-learning potential
 * :doc:`soft <pair_soft>` - Soft (cosine) potential
 * :doc:`sph/heatconduction <pair_sph_heatconduction>` -

doc/src/pair_uf3.rst

@@ -36,7 +36,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 27June2024
 
 The *uf3* style computes the :ref:`Ultra-Fast Force Fields (UF3)
 <Xie23>` potential, a machine-learning interatomic potential. In UF3,

doc/src/read_data.rst

@@ -12,7 +12,7 @@ Syntax
 
 * file = name of data file to read in
 * zero or more keyword/arg pairs may be appended
-* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *group* or *nocoeff* or *fix*
+* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom* or *group* or *nocoeff* or *fix*
 
   .. parsed-literal::
 
@@ -859,6 +859,10 @@ of analysis.
      - atom-ID molecule-ID atom-type x y z
    * - peri
      - atom-ID atom-type volume density x y z
+   * - rheo
+     - atom-ID atom-type status rho x y z
+   * - rheo/thermal
+     - atom-ID atom-type status rho energy x y z
    * - smd
      - atom-ID atom-type molecule volume mass kradius cradius x0 y0 z0 x y z
    * - sph

doc/src/reset_atoms.rst

@@ -32,7 +32,7 @@ Syntax
 
   .. code-block:: LAMMPS
 
-     reset atoms mol group-ID keyword value ...
+     reset_atoms mol group-ID keyword value ...
 
   * group-ID = ID of group of atoms whose molecule IDs will be reset
   * zero or more keyword/value pairs can be appended
@@ -66,16 +66,16 @@ Description
 .. versionadded:: 22Dec2022
 
 The *reset_atoms* command resets the values of a specified atom
-property.  In contrast to the set command, it does this in a
+property.  In contrast to the *set* command, it does this in a
 collective manner which resets the values for many atoms in a
-self-consistent way.  This is often useful when the simulated system
+self-consistent way.  This command is often useful when the simulated
-has undergone significant modifications like adding or removing atoms
+system has undergone significant modifications like adding or removing
-or molecules, joining data files, changing bonds, or large-scale
+atoms or molecules, joining data files, changing bonds, or large-scale
 diffusion.
 
 The new values can be thought of as a *reset*, similar to values atoms
 would have if a new data file were being read or a new simulation
-performed.  Note that the set command also resets atom properties to
+performed.  Note that the *set* command also resets atom properties to
 new values, but it treats each atom independently.
 
 The *property* setting can be *id* or *image* or *mol*.  For *id*, the
@@ -90,7 +90,7 @@ keyword/value settings are given below.
 
 ----------
 
-*Property id*
+Property: *id*
 
 Reset atom IDs for the entire system, including all the global IDs
 stored for bond, angle, dihedral, improper topology data.  This will
@@ -146,7 +146,7 @@ processor have consecutive IDs, as the :doc:`create_atoms
 
 ----------
 
-*Property image*
+Property: *image*
 
 Reset the image flags of atoms so that at least one atom in each
 molecule has an image flag of 0.  Molecular topology is respected so
@@ -191,7 +191,7 @@ flags.
 
 ----------
 
-*Property mol*
+Property: *mol*
 
 Reset molecule IDs for a specified group of atoms based on current
 bond connectivity.  This will typically create a new set of molecule
@@ -203,7 +203,7 @@ For purposes of this operation, molecules are identified by the current
 bond connectivity in the system, which may or may not be consistent with
 the current molecule IDs.  A molecule in this context is a set of atoms
 connected to each other with explicit bonds.  The specific algorithm
-used is the one of :doc:`compute fragment/atom <compute_cluster_atom>`
+used is the one of :doc:`compute fragment/atom <compute_cluster_atom>`.
 Once the molecules are identified and a new molecule ID computed for
 each, this command will update the current molecule ID for all atoms in
 the group with the new molecule ID.  Note that if the group excludes
@@ -266,7 +266,7 @@ The *image* property can only be used when the atom style supports bonds.
 Related commands
 """"""""""""""""
 
-:doc:`compute fragment/atom <compute_cluster_atom>`
+:doc:`compute fragment/atom <compute_cluster_atom>`,
 :doc:`fix bond/react <fix_bond_react>`,
 :doc:`fix bond/create <fix_bond_create>`,
 :doc:`fix bond/break <fix_bond_break>`,

doc/src/set.rst

@@ -120,6 +120,8 @@ Syntax
        *angle* value = numeric angle type or angle type label, for all angles between selected atoms
        *dihedral* value = numeric dihedral type or dihedral type label, for all dihedrals between selected atoms
        *improper* value = numeric improper type or improper type label, for all impropers between selected atoms
+       *rheo/rho* value = density of RHEO particles (mass/distance\^3)
+       *rheo/status* value = status or phase of RHEO particles (unitless)
        *sph/e* value = energy of SPH particles (need units)
          value can be an atom-style variable (see below)
        *sph/cv* value = heat capacity of SPH particles (need units)
@@ -506,6 +508,10 @@ by the *bond types* (\ *angle types*, etc) field in the header of the
 data file read by the :doc:`read_data <read_data>` command.  These
 keywords do not allow use of an atom-style variable.
 
+Keywords *rheo/rho* and *rheo/status* set the density and the status of
+rheo particles. In particular, one can only set the phase in the status
+as described by the :doc:`RHEO howto page <Howto_rheo>`.
+
 Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
 and density of smoothed particle hydrodynamics (SPH) particles.  See
 `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.

doc/src/variable.rst

@@ -67,7 +67,7 @@ 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)
+         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()
          feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
          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
@@ -547,7 +547,7 @@ variables.
 +------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Region functions       | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR)                                                                                                                |
 +------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| 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)                                                                                                                               |
+| 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()                                                                                                                 |
 +------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Feature functions      | is_available(category,feature), is_active(category,feature), is_defined(category,id)                                                                                                                                                                                                                                                              |
 +------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@@ -957,7 +957,7 @@ of points, equally spaced by 1 in their x coordinate: (1,V1), (2,V2),
 length N.  The returned value is the slope of the line.  If the line
 has a single point or is vertical, it returns 1.0e20.
 
-.. versionadded:: TBD
+.. versionadded:: 27June2024
 
 The sort(x) and rsort(x) functions sort the data of the input vector by
 their numeric value: sort(x) sorts in ascending order, rsort(x) sorts
@@ -1042,6 +1042,20 @@ label2type(), but returns 1 if the type label has been assigned,
 otherwise it returns 0.  This function can be used to check if a
 particular type label already exists in the simulation.
 
+.. versionadded:: TBD
+
+The is_timeout() function returns 1 when the :doc:`timer timeout
+<timer>` has expired otherwise it returns 0.  This function can be used
+to check inputs in combination with the :doc:`if command <if>` to
+execute commands after the timer has expired. Example:
+
+.. code-block:: LAMMPS
+
+   variable timeout equal is_timeout()
+   timer timeout 0:10:00 every 10
+   run 10000
+   if ${timeout} then "print 'Timer has expired'"
+
 ----------
 
 Feature Functions

doc/utils/requirements.txt

@@ -1,6 +1,7 @@
 Sphinx >= 5.3.0, <8.0
 sphinxcontrib-spelling
 sphinxcontrib-jquery
+sphinx-design
 git+https://github.com/akohlmey/sphinx-fortran@parallel-read
 sphinx-tabs>=3.4.1
 breathe

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

@@ -41,7 +41,7 @@ sys.path.append(os.path.join(LAMMPS_DOC_DIR, 'utils', 'sphinx-config', '_themes'
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-needs_sphinx = '5.2.0'
+needs_sphinx = '5.3.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -57,6 +57,7 @@ extensions = [
     'table_from_list',
     'tab_or_note',
     'breathe',
+    'sphinx_design'
 ]
 
 images_config = {
@@ -68,7 +69,7 @@ images_config = {
 templates_path = ['_templates']
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = {'.rst': 'restructuredtext'}
 
 # The encoding of source files.
 #source_encoding = 'utf-8-sig'

doc/utils/sphinx-config/false_positives.txt

@@ -393,6 +393,7 @@ buf
 builtin
 Bulacu
 Bulatov
+Bulkley
 Bureekaew
 burlywood
 Bussi
@@ -564,6 +565,7 @@ cond
 conda
 Conda
 Condens
+conductivities
 conf
 config
 configfile
@@ -1099,6 +1101,7 @@ excv
 exe
 executables
 extep
+extractable
 extrema
 extxyz
 exy
@@ -1173,6 +1176,7 @@ finitecutflag
 Finnis
 Fiorin
 fitpod
+fivebody
 fixID
 fj
 Fji
@@ -1439,6 +1443,7 @@ henrich
 Henrich
 Hermitian
 Herrmann
+Hershchel
 Hertizian
 hertzian
 Hertzsch
@@ -1830,6 +1835,7 @@ Kspace
 KSpace
 KSpaceStyle
 Kspring
+kstyle
 kT
 kTequil
 kth
@@ -2270,6 +2276,7 @@ modelled
 modelling
 Modelling
 Modine
+modularity
 moduli
 mofff
 MOFFF
@@ -2487,6 +2494,7 @@ Neumann
 Nevent
 nevery
 Nevery
+Nevins
 newfile
 Newns
 newtype
@@ -2897,6 +2905,7 @@ Pmolrotate
 Pmoltrans
 pN
 png
+podd
 Podhorszki
 Poiseuille
 poisson
@@ -3065,6 +3074,7 @@ quatw
 queryargs
 Queteschiner
 quickmin
+quintic
 qw
 qx
 qy
@@ -3076,6 +3086,7 @@ radialscreenedspin
 radialspin
 radian
 radians
+radiative
 radj
 Rafferty
 rahman
@@ -3179,6 +3190,7 @@ rg
 Rg
 Rhaphson
 Rhe
+rheo
 rheological
 rheology
 rhodo
@@ -3266,6 +3278,7 @@ rsort
 rsq
 rst
 rstyle
+rsurf
 Rubensson
 Rubia
 Rud
@@ -3370,6 +3383,7 @@ setmask
 Setmask
 setpoint
 setvel
+sevenbody
 sfftw
 sfree
 Sg
@@ -3420,6 +3434,7 @@ SiO
 Siochi
 Sirk
 Sival
+sixbody
 sizeI
 sizeJ
 sizex
@@ -3647,6 +3662,7 @@ Telsa
 tempCorrCoeff
 templated
 Templeton
+Tencer
 Tequil
 ters
 tersoff
@@ -3735,7 +3751,6 @@ tokyo
 tol
 tomic
 toolchain
-toolset
 topologies
 Toporov
 Torder
@@ -3813,6 +3828,7 @@ typeJ
 typelabel
 typeN
 typesafe
+typestr
 Tz
 Tzou
 ub
@@ -3993,6 +4009,7 @@ Vries
 Vsevolod
 Vsmall
 Vstream
+vstyle
 vtarget
 vtk
 VTK

examples/COUPLE/plugin/liblammpsplugin.c

@@ -101,6 +101,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
   ADDSYM(extract_setting);
   ADDSYM(extract_global_datatype);
   ADDSYM(extract_global);
+  ADDSYM(extract_pair_dimension);
+  ADDSYM(extract_pair);
   ADDSYM(map_atom);
 
   ADDSYM(extract_atom_datatype);

examples/COUPLE/plugin/liblammpsplugin.h

@@ -144,11 +144,13 @@ struct _liblammpsplugin {
   int (*get_mpi_comm)(void *);
 
   int (*extract_setting)(void *, const char *);
-  int *(*extract_global_datatype)(void *, const char *);
+  int (*extract_global_datatype)(void *, const char *);
   void *(*extract_global)(void *, const char *);
-  void *(*map_atom)(void *, const void *);
+  int (*extract_pair_dimension)(void *, const char *);
+  void *(*extract_pair)(void *, const char *);
+  int (*map_atom)(void *, const void *);
 
-  int *(*extract_atom_datatype)(void *, const char *);
+  int (*extract_atom_datatype)(void *, const char *);
   void *(*extract_atom)(void *, const char *);
 
   void *(*extract_compute)(void *, const char *, int, int);

examples/PACKAGES/electrode/madelung/.gitignore

@@ -1,2 +1,3 @@
 *.csv
 *.txt
+*.lammpstrj

examples/PACKAGES/electrode/madelung/eval.py

@@ -17,14 +17,22 @@ q_ref = float(ref_line[3])
 inv11_ref = float(ref_line[4])
 inv12_ref = float(ref_line[5])
 b1_ref = float(ref_line[6])
+felec1_ref = float(ref_line[8])
+felyt1_ref = float(ref_line[10])
+press_ref = float(ref_line[12])
 
 # out.csv
 with open(sys.argv[2]) as f:
     out_line = f.readlines()[-1].split(", ")
 e_out = float(out_line[0])
 q_out = float(out_line[1])
+press_out = float(out_line[2])
 
-out_lines = [("energy", e_ref, e_out), ("charge", q_ref, q_out)]
+out_lines = [
+    ("energy", e_ref, e_out),
+    ("charge", q_ref, q_out),
+    ("pressure", press_ref, press_out),
+]
 
 # vec.csv
 vec_file = "vec.csv"
@@ -44,6 +52,14 @@ if op.isfile(inv_file):
     inv12_out = float(inv_line[1])
     out_lines.append(("inv11", inv11_ref, inv11_out))
 
+# forces.lammpstrj
+force_file = "forces.lammpstrj"
+with open(force_file) as f:
+    lines = f.readlines()[9:]
+    for name, i, f_ref in [("felec1", "1", felec1_ref), ("felyt1", "3", felyt1_ref)]:
+        f_out = next(float(y[3]) for x in lines if (y := x.split()) and y[0] == i)
+        out_lines.append((name, f_ref, f_out))
+
 lines = []
 for label, ref, out in out_lines:
     error = rel_error(out, ref)

examples/PACKAGES/electrode/madelung/in.eta_cg

@@ -8,7 +8,7 @@ thermo_style custom step pe c_qbot c_qtop
 fix feta all property/atom d_eta ghost on
 set group bot d_eta 0.5
 set group top d_eta 3.0
-fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta algo cg 1e-6
+fix conp bot electrode/conp 0 NULL couple top 1 symm on eta d_eta algo cg 1e-6
 
 run 0
 

examples/PACKAGES/electrode/madelung/in.eta_mix

@@ -8,7 +8,7 @@ thermo_style custom step pe c_qbot c_qtop
 fix feta all property/atom d_eta ghost on
 set group bot d_eta 0.5
 set group top d_eta 3.0
-fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
+fix conp bot electrode/conp 0 NULL couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
 
 run 0
 

examples/PACKAGES/electrode/madelung/plate_cap.py

@@ -1,12 +1,17 @@
 #!/usr/bin/env python3
 
+import time
+
 import numpy as np
 from scipy.special import erf
 
 SQRT2 = np.sqrt(2)
+SQRTPI_INV = 1 / np.sqrt(np.pi)
 COULOMB = 332.06371  #  Coulomb constant in Lammps 'real' units
 QE2F = 23.060549
+NKTV2P = 68568.415  # pressure in 'real' units
 LENGTH = 10000  # convergence parameter
+LZ = 20
 
 
 def lattice(length):
@@ -26,6 +31,25 @@ def b_element(r, q, eta):
     return q * erf(eta * r) / r
 
 
+def force_gauss(r, qq, eta):
+    etar = eta * r
+    return (qq / np.square(r)) * (
+        erf(etar) - 2 * etar * SQRTPI_INV * np.exp(-np.square(etar))
+    )
+
+
+def force_point(r, qq):
+    return qq / np.square(r)
+
+
+def force_component(dx, d, qq, eta=None):
+    if eta:
+        return np.sum(dx / d * force_gauss(d, qq, eta))
+    else:
+        return np.sum(dx / d * force_point(d, qq))
+
+
+time_start = time.perf_counter()
 a = 1  # nearest neighbor distance i.e. lattice constant / sqrt(2)
 x_elec = [-2, 2]
 x_elyt = [-1, 1]
@@ -36,8 +60,20 @@ v = np.array([-0.5, 0.5]) * (QE2F / COULOMB)
 # distances to images within electrode and to opposite electrode
 distances = a * np.linalg.norm(lattice(LENGTH), axis=1)
 opposite_distances = np.sqrt(np.square(distances) + distance_plates**2)
+image_distances = []
+for x in x_elec:
+    image_distances.append([])
+    for y in x_elyt:
+        image_distances[-1].append(np.sqrt(np.square(distances) + np.abs(y - x) ** 2))
+image_elyt_distances = [[None for _ in range(len(x_elyt))] for _ in range(len(x_elyt))]
+for i, (xi, qi) in enumerate(zip(x_elyt, q_elyt)):
+    for j, (xj, qj) in list(enumerate(zip(x_elyt, q_elyt)))[i + 1 :]:
+        image_elyt_distances[i][j] = np.sqrt(
+            np.square(distances) + np.abs(xj - xi) ** 2
+        )
 
 for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
+    # for name, eta_elec in [("", [2.0, 2.0])]:
     eta_mix = np.prod(eta_elec) / np.sqrt(np.sum(np.square(eta_elec)))
     # self interaction and within original box
     A_11 = np.sqrt(2 / np.pi) * eta_elec[0]
@@ -55,22 +91,18 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
 
     # electrode-electrolyte interaction
     b = []
-    for x, eta in zip(x_elec, eta_elec):
+    for i, (x, eta) in enumerate(zip(x_elec, eta_elec)):
         bi = 0
-        for y, q in zip(x_elyt, q_elyt):
+        for j, (y, q) in enumerate(zip(x_elyt, q_elyt)):
-            d = abs(y - x)
+            bi += b_element(np.abs(y - x), q, eta)
-            bi += b_element(d, q, eta)
+            bi += 4 * np.sum(b_element(image_distances[i][j], q, eta))
-            image_distances = np.sqrt(np.square(distances) + d**2)
-            bi += 4 * np.sum(b_element(image_distances, q, eta))
         b.append(bi)
     b = np.array(b)
 
     # electrolyte-electrolyte energy
     elyt_11 = 4 * np.sum(1 / distances)
     distance_elyt = x_elyt[1] - x_elyt[0]
-    elyt_12 = 1 / distance_elyt + 4 * np.sum(
+    elyt_12 = 1 / distance_elyt + 4 * np.sum(1 / image_elyt_distances[0][1])
-        1 / np.sqrt(np.square(distances) + distance_elyt**2)
-    )
     elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]])
     energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt))
 
@@ -78,9 +110,48 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
     q = np.dot(inv, v - b)
     energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt)
 
+    # forces in out-of-plane direction
+    f_elec = np.zeros(len(x_elec))
+    f_elyt = np.zeros(len(x_elyt))
+    # electrode-electrode
+    dx = x_elec[1] - x_elec[0]
+    fij_box = force_component(dx, np.abs(dx), q[0] * q[1], eta_mix)
+    fij_img = 4 * force_component(dx, opposite_distances, q[0] * q[1], eta_mix)
+    f_elec[0] -= fij_box + fij_img
+    f_elec[1] += fij_box + fij_img
+    # electrode-electrolyte
+    for i, (xi, qi, etai) in enumerate(zip(x_elec, q, eta_elec)):
+        for j, (xj, qj) in enumerate(zip(x_elyt, q_elyt)):
+            dx = xj - xi
+            fij_box = force_component(dx, np.abs(dx), qi * qj, etai)
+            fij_img = 4 * force_component(dx, image_distances[i][j], qi * qj, etai)
+            f_elec[i] -= fij_box + fij_img
+            f_elyt[j] += fij_box + fij_img
+    # electrolyte-electrolyte
+    for i, (xi, qi) in enumerate(zip(x_elyt, q_elyt)):
+        for j, (xj, qj) in list(enumerate(zip(x_elyt, q_elyt)))[i + 1 :]:
+            dx = xj - xi
+            fij_box = force_component(dx, np.abs(dx), qi * qj)
+            fij_img = 4 * force_component(dx, image_elyt_distances[i][j], qi * qj)
+            f_elyt[i] -= fij_img + fij_box
+            f_elyt[j] += fij_img + fij_box
+    # force units
+    assert np.abs(np.sum(f_elec) + np.sum(f_elyt)) < 1e-8
+    f_elec *= COULOMB
+    f_elyt *= COULOMB
+
+    # Virial
+    volume = a**2 * LZ
+    virial = 0.0
+    for x, f in [(x_elec, f_elec), (x_elyt, f_elyt)]:
+        virial += np.dot(x, f)
+    pressure = NKTV2P * virial / volume
+
     with open(f"plate_cap{name}.csv", "w") as f:
         f.write(
-            "length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A, b1 / e/A, b2 / e/A\n"
+            "length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A"
+            + ", b1 / e/A, b2 / e/A, felec1 / kcal/mol/A, felec2 / kcal/mol/A"
+            + ", felyt1 / kcal/mol/A, felyt2 / kcal/mol/A, press\n"
         )
         f.write(
             ", ".join(
@@ -93,7 +164,14 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
                     f"{inv[0, 1]:.10f}",
                     f"{b[0]:.8f}",
                     f"{b[1]:.8f}",
+                    f"{f_elec[0]:.5f}",
+                    f"{f_elec[1]:.5f}",
+                    f"{f_elyt[0]:.5f}",
+                    f"{f_elyt[1]:.5f}",
+                    f"{pressure:.2f}",
                 ]
             )
             + "\n"
         )
+time_end = time.perf_counter()
+print(f"{time_end - time_start:0.4f} seconds")

examples/PACKAGES/electrode/madelung/settings.mod

@@ -19,4 +19,8 @@ compute qtop top reduce sum v_q
 compute compute_pe all pe
 variable vpe equal c_compute_pe
 variable charge equal c_qtop
-fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
+compute press all pressure NULL virial
+variable p3 equal c_press[3]
+fix fxprint all print 1 "${vpe}, ${charge}, ${p3}" file "out.csv"
+
+dump dump_forces all custom 1 forces.lammpstrj id fx fy fz

examples/PACKAGES/electrode/piston/in.piston

@@ -42,7 +42,11 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
 
 # equilibrate z-coordinate of upper electrode while keeping the electrode rigid
 fix fxforce_wa wall setforce 0.0 0.0 NULL
-fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
+variable atm equal 1/68568.415 # 1/force->nktv2p
+variable area equal (xhi-xlo)*(yhi-ylo)
+variable wall_force equal -v_atm*v_area/count(wall)
+print "Wall force per atom: ${wall_force}"
+fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
 fix fxdrag     wall viscous 100
 fix fxrigid    wall rigid/nve single
 

examples/PACKAGES/electrode/piston/log.22May2024.piston.g++.1

@@ -1,4 +1,5 @@
-LAMMPS (3 Nov 2022)
+LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
+  using 1 OpenMP thread(s) per MPI task
 # The intention is to find the average position of one wall at atmospheric
 # pressure.  The output is the wall position over time which can be used to
 # find the average position for a run with fixed wall position.
@@ -40,8 +41,8 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-3 neighbors
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
-  special bonds CPU = 0.001 seconds
+  special bonds CPU = 0.000 seconds
-  read_data CPU = 0.011 seconds
+  read_data CPU = 0.012 seconds
 
 # ----------------- Settings Section -----------------
 
@@ -77,7 +78,13 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
 
 # equilibrate z-coordinate of upper electrode while keeping the electrode rigid
 fix fxforce_wa wall setforce 0.0 0.0 NULL
-fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
+variable atm equal 1/68568.415 # 1/force->nktv2p
+variable area equal (xhi-xlo)*(yhi-ylo)
+variable wall_force equal -v_atm*v_area/count(wall)
+print "Wall force per atom: ${wall_force}"
+Wall force per atom: -0.000109285996244287
+fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
+fix fxpressure wall aveforce 0 0 -0.000109285996244287 
 fix fxdrag     wall viscous 100
 fix fxrigid    wall rigid/nve single
   1 rigid bodies with 48 atoms
@@ -134,7 +141,7 @@ PPPM/electrode initialization ...
   stencil order = 5
   estimated absolute RMS force accuracy = 0.02930901
   estimated relative force accuracy = 8.8263214e-05
-  using double precision MKL FFT
+  using double precision FFTW3
   3d grid and FFT values/proc = 15884 6480
 Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
 Neighbor list info ...
@@ -157,54 +164,54 @@ Neighbor list info ...
 Per MPI rank memory allocation (min/avg/max) = 11.7 | 11.7 | 11.7 Mbytes
    Step     c_temp_mobile      c_qwa          c_qau        v_top_wall  
          0   303.38967     -0.042963484    0.042963484    21.4018      
-      5000   285.08828     -0.26105255     0.26105255     25.155629    
+      5000   311.85363      0.03543775    -0.03543775     24.79665     
-     10000   323.19176     -0.26264003     0.26264003     24.541676    
+     10000   285.91321     -0.16873703     0.16873703     23.103088    
-     15000   310.479       -0.27318148     0.27318148     23.141522    
+     15000   295.39476     -0.44424612     0.44424612     23.767107    
-     20000   295.18544     -0.11313444     0.11313444     23.828735    
+     20000   296.12969     -0.14120993     0.14120993     23.96361     
-     25000   295.38607     -0.25433086     0.25433086     23.673314    
+     25000   306.59629     -0.29333182     0.29333182     23.884488    
-     30000   288.0613      -0.30099901     0.30099901     23.438086    
+     30000   297.98559     -0.10749684     0.10749684     23.73316     
-     35000   278.5591      -0.15823576     0.15823576     24.311915    
+     35000   297.98503     -0.11809975     0.11809975     23.984669    
-     40000   303.95751     -0.19941381     0.19941381     23.69594     
+     40000   300.26292     -0.32784184     0.32784184     23.462748    
-     45000   279.026       -0.1659962      0.1659962      23.588604    
+     45000   295.68441     -0.25940165     0.25940165     23.516403    
-     50000   298.79278     -0.28866703     0.28866703     23.372508    
+     50000   315.12883     -0.36037614     0.36037614     23.627879    
-     55000   301.03353     -0.078370381    0.078370381    23.192985    
+     55000   290.55151     -0.0032838106   0.0032838106   23.684931    
-     60000   306.77965     -0.12807205     0.12807205     23.968574    
+     60000   316.4625      -0.17245368     0.17245368     24.126883    
-     65000   309.86008     -0.27162663     0.27162663     23.616704    
+     65000   296.79343     -0.054061851    0.054061851    23.695094    
-     70000   287.31116     -0.029751882    0.029751882    23.667495    
+     70000   305.99923     -0.11363801     0.11363801     23.55476     
-     75000   312.48654     -0.10759866     0.10759866     23.504105    
+     75000   297.40131     -0.27054153     0.27054153     23.928994    
-     80000   309.94267     -0.2558548      0.2558548      23.810576    
+     80000   306.54811     -0.25409719     0.25409719     23.869448    
-     85000   328.04389     -0.1575471      0.1575471      24.013437    
+     85000   303.95231     -0.17895561     0.17895561     23.658833    
-     90000   302.9806      -0.032002164    0.032002164    24.264432    
+     90000   313.43739     -0.059036514    0.059036514    23.36056     
-     95000   294.20804     -0.27797238     0.27797238     23.291758    
+     95000   290.3077      -0.31394478     0.31394478     23.885538    
-    100000   307.63019     -0.19047448     0.19047448     23.632147    
+    100000   297.5156      -0.30730083     0.30730083     23.511674    
-Loop time of 530.844 on 1 procs for 100000 steps with 726 atoms
+Loop time of 1586.06 on 1 procs for 100000 steps with 726 atoms
 
-Performance: 32.552 ns/day, 0.737 hours/ns, 188.379 timesteps/s, 136.763 katom-step/s
+Performance: 10.895 ns/day, 2.203 hours/ns, 63.049 timesteps/s, 45.774 katom-step/s
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
+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    | 190.47     | 190.47     | 190.47     |   0.0 | 35.88
+Pair    | 460.91     | 460.91     | 460.91     |   0.0 | 29.06
-Bond    | 0.10754    | 0.10754    | 0.10754    |   0.0 |  0.02
+Bond    | 0.047873   | 0.047873   | 0.047873   |   0.0 |  0.00
-Kspace  | 73.179     | 73.179     | 73.179     |   0.0 | 13.79
+Kspace  | 341.4      | 341.4      | 341.4      |   0.0 | 21.53
-Neigh   | 24.209     | 24.209     | 24.209     |   0.0 |  4.56
+Neigh   | 52.868     | 52.868     | 52.868     |   0.0 |  3.33
-Comm    | 1.6857     | 1.6857     | 1.6857     |   0.0 |  0.32
+Comm    | 5.2321     | 5.2321     | 5.2321     |   0.0 |  0.33
-Output  | 0.0016861  | 0.0016861  | 0.0016861  |   0.0 |  0.00
+Output  | 0.00099102 | 0.00099102 | 0.00099102 |   0.0 |  0.00
-Modify  | 240.23     | 240.23     | 240.23     |   0.0 | 45.26
+Modify  | 724.63     | 724.63     | 724.63     |   0.0 | 45.69
-Other   |            | 0.9595     |            |       |  0.18
+Other   |            | 0.9741     |            |       |  0.06
 
 Nlocal:            726 ave         726 max         726 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:           2335 ave        2335 max        2335 min
+Nghost:           2336 ave        2336 max        2336 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:         120271 ave      120271 max      120271 min
+Neighs:         120321 ave      120321 max      120321 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 120271
+Total # of neighbors = 120321
-Ave neighs/atom = 165.66253
+Ave neighs/atom = 165.7314
 Ave special neighs/atom = 1.7355372
-Neighbor list builds = 7722
+Neighbor list builds = 7670
 Dangerous builds = 0
 write_data "data.piston.final"
 System init for write_data ...
@@ -213,11 +220,11 @@ PPPM/electrode initialization ...
   G vector (1/distance) = 0.32814871
   grid = 12 15 36
   stencil order = 5
-  estimated absolute RMS force accuracy = 0.029311365
+  estimated absolute RMS force accuracy = 0.029311329
-  estimated relative force accuracy = 8.8270304e-05
+  estimated relative force accuracy = 8.8270197e-05
-  using double precision MKL FFT
+  using double precision FFTW3
   3d grid and FFT values/proc = 15884 6480
 Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
 
 Average conjugate gradient steps: 1.981
-Total wall time: 0:08:50
+Total wall time: 0:26:26