diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 0687b54fcb..0bd4136c21 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -133,6 +133,24 @@ foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 
+######################################################
+# download and unpack support binaries for compilation
+# of windows binaries.
+######################################################
+if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+  set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")
+  file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
+          EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
+  execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+  if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")
+    set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")
+  elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")
+    set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")
+  endif()
+  set(OpenCL_INCLUDE_DIR "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")
+endif()
+
+######################################################
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
@@ -148,6 +166,7 @@ if(PKG_USER-ADIOS)
 endif()
 
 # do MPI detection after language activation, if MPI for these language is required
+set(MPI_CXX_SKIP_MPICXX TRUE)
 find_package(MPI QUIET)
 option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 if(BUILD_MPI)
@@ -175,11 +194,13 @@ add_definitions(-DLAMMPS_${LAMMPS_SIZES})
 set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_${LAMMPS_SIZES}")
 
 # posix_memalign is not available on Windows
-if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+  set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE)
+else()
   set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable")
-  if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
-    add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
-  endif()
+endif()
+if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
+  add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
 endif()
 
 option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
@@ -219,8 +240,7 @@ if(BUILD_OMP)
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
 endif()
 
-
-if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUIP OR PKG_LATTE)
+if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
@@ -230,6 +250,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUI
     enable_language(Fortran)
     file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
     add_library(linalg STATIC ${LAPACK_SOURCES})
+    set(BLAS_LIBRARIES linalg)
     set(LAPACK_LIBRARIES linalg)
   else()
     list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
@@ -497,10 +518,43 @@ if(BUILD_LIB)
   if(LAMMPS_DEPS)
     add_dependencies(lammps ${LAMMPS_DEPS})
   endif()
+  set(LAMMPS_CXX_HEADERS
+    ${LAMMPS_SOURCE_DIR}/angle.h
+    ${LAMMPS_SOURCE_DIR}/atom.h
+    ${LAMMPS_SOURCE_DIR}/bond.h
+    ${LAMMPS_SOURCE_DIR}/citeme.h
+    ${LAMMPS_SOURCE_DIR}/comm.h
+    ${LAMMPS_SOURCE_DIR}/compute.h
+    ${LAMMPS_SOURCE_DIR}/dihedral.h
+    ${LAMMPS_SOURCE_DIR}/domain.h
+    ${LAMMPS_SOURCE_DIR}/error.h
+    ${LAMMPS_SOURCE_DIR}/fix.h
+    ${LAMMPS_SOURCE_DIR}/force.h
+    ${LAMMPS_SOURCE_DIR}/group.h
+    ${LAMMPS_SOURCE_DIR}/improper.h
+    ${LAMMPS_SOURCE_DIR}/input.h
+    ${LAMMPS_SOURCE_DIR}/kspace.h
+    ${LAMMPS_SOURCE_DIR}/lammps.h
+    ${LAMMPS_SOURCE_DIR}/lattice.h
+    ${LAMMPS_SOURCE_DIR}/lmppython.h
+    ${LAMMPS_SOURCE_DIR}/memory.h
+    ${LAMMPS_SOURCE_DIR}/modify.h
+    ${LAMMPS_SOURCE_DIR}/neighbor.h
+    ${LAMMPS_SOURCE_DIR}/neigh_list.h
+    ${LAMMPS_SOURCE_DIR}/output.h
+    ${LAMMPS_SOURCE_DIR}/pair.h
+    ${LAMMPS_SOURCE_DIR}/pointers.h
+    ${LAMMPS_SOURCE_DIR}/region.h
+    ${LAMMPS_SOURCE_DIR}/timer.h
+    ${LAMMPS_SOURCE_DIR}/universe.h
+    ${LAMMPS_SOURCE_DIR}/update.h
+    ${LAMMPS_SOURCE_DIR}/variable.h)
+
   set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
   set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
   install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
   install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+  install(FILES ${LAMMPS_CXX_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
   configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
   configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
@@ -535,6 +589,7 @@ if(BUILD_TOOLS)
     enable_language(Fortran)
     add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
     target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+    install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
   endif()
 
   enable_language(C)
@@ -551,11 +606,11 @@ include(Documentation)
 ###############################################################################
 # Install potential and force field files in data directory
 ###############################################################################
-set(LAMMPS_INSTALL_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)
-install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_POTENTIALS_DIR})
-
-set(LAMMPS_INSTALL_FRC_FILES_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/frc_files)
-install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files/ DESTINATION ${LAMMPS_INSTALL_FRC_FILES_DIR})
+set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps)
+install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR})
+if(BUILD_TOOLS)
+  install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR})
+endif()
 
 configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
 configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)
diff --git a/cmake/Modules/FindKIM-API.cmake b/cmake/Modules/FindKIM-API.cmake
index 5108b0f98c..17c195e62f 100644
--- a/cmake/Modules/FindKIM-API.cmake
+++ b/cmake/Modules/FindKIM-API.cmake
@@ -37,6 +37,26 @@
 # KIM-API-CMAKE_Fortran_COMPILER
 #
 
+function(_KIMAPI_GET_VERSION _OUT_ver _version_hdr)
+  if(NOT EXISTS ${_version_hdr})
+    message(FATAL_ERROR "Header file ${_version_hdr} not found (check value of KIM-API_INCLUDE_DIR)")
+  endif()
+  foreach(_var KIM_VERSION_MAJOR KIM_VERSION_MINOR KIM_VERSION_PATCH)  
+    file(STRINGS ${_version_hdr} _contents REGEX "#define ${_var}[ \t]+")
+    if(_contents)
+      string(REGEX REPLACE ".*#define ${_var}[ \t]+([0-9]+).*" "\\1" _${_var} "${_contents}")
+      if(${_${_var}} STREQUAL "")
+        message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, got empty return!")
+      elseif(NOT ${_${_var}} MATCHES "^[0-9]+$")
+        message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, excepted a number but got ${_${_var}}!")
+      endif()
+    else()
+      message(FATAL_ERROR "No ${_var} line found in include file ${_version_hdr}")
+    endif()
+  endforeach()
+  set(${_OUT_ver} ${_KIM_VERSION_MAJOR}.${_KIM_VERSION_MINOR}.${_KIM_VERSION_PATCH} PARENT_SCOPE)
+endfunction()
+
 if(KIM-API_FIND_QUIETLY)
   set(REQ_OR_QUI "QUIET")
 else()
@@ -54,6 +74,12 @@ if(KIM-API_FOUND)
   pkg_get_variable(KIM-API_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
 endif()
 
+if(KIM-API_INCLUDEDIR)
+  _KIMAPI_GET_VERSION(KIM-API_VERSION ${KIM-API_INCLUDEDIR}/KIM_Version.h)
+else()
+  set(KIM-API_VERSION 0)
+endif()
+
 # handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE
 # if all listed variables are TRUE
-find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES)
+find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES VERSION_VAR KIM-API_VERSION)
diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake
index 8815f73881..8d17225760 100644
--- a/cmake/Modules/Packages/KIM.cmake
+++ b/cmake/Modules/Packages/KIM.cmake
@@ -1,4 +1,5 @@
 if(PKG_KIM)
+  set(KIM-API_MIN_VERSION 2.1)
   find_package(CURL)
   if(CURL_FOUND)
     include_directories(${CURL_INCLUDE_DIRS})
@@ -7,8 +8,18 @@ if(PKG_KIM)
   endif()
   find_package(KIM-API QUIET)
   if(KIM-API_FOUND)
-    set(DOWNLOAD_KIM_DEFAULT OFF)
+    if (KIM-API_VERSION VERSION_LESS ${KIM-API_MIN_VERSION})
+      if ("${DOWNLOAD_KIM}" STREQUAL "")
+        message(WARNING "Unsuitable KIM-API version \"${KIM-API_VERSION}\" found, but required is at least \"${KIM-API_MIN_VERSION}\".  Default behavior set to download and build our own.")
+      endif()
+      set(DOWNLOAD_KIM_DEFAULT ON)
+    else()
+      set(DOWNLOAD_KIM_DEFAULT OFF)
+    endif()
   else()
+    if ("${DOWNLOAD_KIM}" STREQUAL "")
+      message(WARNING "KIM-API package not found.  Default behavior set to download and build our own")
+    endif()
     set(DOWNLOAD_KIM_DEFAULT ON)
   endif()
   option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
@@ -17,12 +28,16 @@ if(PKG_KIM)
       message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
     endif()
     message(STATUS "KIM-API download requested - we will build our own")
-    enable_language(C)
-    enable_language(Fortran)
+    include(CheckLanguage)
     include(ExternalProject)
+    enable_language(C)
+    check_language(Fortran)
+    if(NOT CMAKE_Fortran_COMPILER)
+      message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
+    endif()
     ExternalProject_Add(kim_build
-      URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz
-      URL_MD5 537d9c0abd30f85b875ebb584f9143fa
+      URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
+      URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
       BINARY_DIR build
       CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
                  -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
@@ -35,7 +50,7 @@ if(PKG_KIM)
     set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
     list(APPEND LAMMPS_DEPS kim_build)
   else()
-    find_package(KIM-API REQUIRED)
+    find_package(KIM-API ${KIM-API_MIN_VERSION} REQUIRED)
   endif()
   list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
   include_directories(${KIM-API_INCLUDE_DIRS})
diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake
index cd4dd21cd7..bc3ef59e73 100644
--- a/cmake/Modules/Packages/KOKKOS.cmake
+++ b/cmake/Modules/Packages/KOKKOS.cmake
@@ -23,6 +23,7 @@ if(PKG_KOKKOS)
                          ${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
 
@@ -40,6 +41,7 @@ if(PKG_KOKKOS)
   # register kokkos-only styles
   RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
   RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
+  RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h)
 
   if(PKG_USER-DPD)
     get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake
index 500558fc72..5c35e13bda 100644
--- a/cmake/Modules/Packages/USER-PLUMED.cmake
+++ b/cmake/Modules/Packages/USER-PLUMED.cmake
@@ -1,11 +1,23 @@
 if(PKG_USER-PLUMED)
-  find_package(GSL REQUIRED)
   set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
   set(PLUMED_MODE_VALUES static shared runtime)
   set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
   validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
   string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
 
+  set(PLUMED_LINK_LIBS "")
+  if(PLUMED_MODE STREQUAL "STATIC")
+    find_package(LAPACK REQUIRED)
+    find_package(BLAS REQUIRED)
+    find_package(GSL REQUIRED)
+    list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
+    list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${GSL_LIBRARIES})
+    find_package(ZLIB QUIET)
+    if(ZLIB_FOUND)
+      list(APPEND PLUMED_LINK_LIBS ${ZLIB_LIBRARIES})
+    endif()
+  endif()
+
   find_package(PkgConfig QUIET)
   set(DOWNLOAD_PLUMED_DEFAULT ON)
   if(PKG_CONFIG_FOUND)
@@ -37,8 +49,8 @@ if(PKG_USER-PLUMED)
     message(STATUS "PLUMED download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(plumed_build
-      URL https://github.com/plumed/plumed2/releases/download/v2.5.1/plumed-src-2.5.1.tgz
-      URL_MD5 c2a7b519e32197a120cdf47e0f194f81
+      URL https://github.com/plumed/plumed2/releases/download/v2.5.2/plumed-src-2.5.2.tgz
+      URL_MD5 bd2f18346c788eb54e1e52f4f6acf41a
       BUILD_IN_SOURCE 1
       CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                                ${CONFIGURE_REQUEST_PIC}
@@ -53,11 +65,11 @@ if(PKG_USER-PLUMED)
     list(APPEND LAMMPS_DEPS plumed_build)
     if(PLUMED_MODE STREQUAL "STATIC")
       add_definitions(-D__PLUMED_WRAPPER_CXX=1)
-      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${GSL_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_DL_LIBS})
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${PLUMED_LINK_LIBS} ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "SHARED")
-      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so ${CMAKE_DL_LIBS})
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} ${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
-      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so)
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
       list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
     endif()
     set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
@@ -70,7 +82,7 @@ if(PKG_USER-PLUMED)
     elseif(PLUMED_MODE STREQUAL "SHARED")
       include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
-      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel.so)
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
       include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
     endif()
     list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})
diff --git a/cmake/Modules/Packages/VORONOI.cmake b/cmake/Modules/Packages/VORONOI.cmake
index 5ce974a7ae..89fa70bf98 100644
--- a/cmake/Modules/Packages/VORONOI.cmake
+++ b/cmake/Modules/Packages/VORONOI.cmake
@@ -18,8 +18,12 @@ if(PKG_VORONOI)
     else()
       set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
     endif()
-    string(APPEND VORO_BUILD_CFLAGS ${CMAKE_CXX_FLAGS})
-    set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
+    if(APPLE)
+      get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
+      set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
+    else()
+      set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
+    endif()
 
     ExternalProject_Add(voro_build
       URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
diff --git a/cmake/README.md b/cmake/README.md
index c11326f9d5..01b6f6a60e 100644
--- a/cmake/README.md
+++ b/cmake/README.md
@@ -33,12 +33,17 @@ tasks, act as a reference and provide examples of typical use cases.
       * [Package-Specific Configuration Options](#package-specific-configuration-options)
          * [KSPACE Package](#kspace-package)
          * [MKL](#mkl)
-         * [FFTW2](#fftw2)
          * [FFTW3](#fftw3)
+         * [BLAS](#blas)
          * [LAPACK](#lapack)
          * [PYTHON Package](#python-package)
          * [GPU Package](#gpu-package)
+         * [MESSAGE Package](#message-package)
+         * [MSCG Package](#mscg-package)
          * [VORONOI Package](#voronoi-package)
+         * [USER-LATTE Package](#user-latte-package)
+         * [USER-PLUMED Package](#user-plumed-package)
+         * [USER-SCAFACOS Package](#user-scafacos-package)
          * [USER-SMD Package](#user-smd-package)
       * [Optional Features](#optional-features)
          * [zlib support](#zlib-support)
@@ -50,8 +55,6 @@ tasks, act as a reference and provide examples of typical use cases.
          * [Building with GNU Compilers](#building-with-gnu-compilers)
          * [Building with Intel Compilers](#building-with-intel-compilers)
          * [Building with LLVM/Clang Compilers](#building-with-llvmclang-compilers)
-      * [Examples](#examples)
-
 
 ## Quick Start for the Impatient
 If you want to skip ahead and just run the compilation using `cmake`, please
@@ -205,8 +208,10 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   <td>Controls if debugging symbols are added to the generated binaries</td>
   <td>
   <dl>
-  <dt><code>Release</code> (default)</dt>
+  <dt><code>RelWithDebInfo (default)</code></dt>
+  <dt><code>Release</code></dt>
   <dt><code>Debug</code></dt>
+  <dt><code>MinSizeRel</code></dt>
   </dl>
   </td>
 </tr>
@@ -249,6 +254,16 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
+  <td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>LAMMPS_MEMALIGN</code></td>
   <td>controls the alignment of blocks of memory allocated by LAMMPS</td>
@@ -271,7 +286,16 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
 </tr>
 <tr>
   <td><code>LAMMPS_MACHINE</code></td>
-  <td>allows appending a machine suffix to the generate LAMMPS binary</td>
+  <td>allows appending a machine suffix to the generated LAMMPS binary</td>
+  <td>
+  <dl>
+    <dt>*none*  (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_LIB_SUFFIX</code></td>
+  <td>allows appending a suffix to the generated LAMMPS library</td>
   <td>
   <dl>
     <dt>*none*  (default)</dt>
@@ -319,8 +343,8 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </td>
 </tr>
 <tr>
-  <td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
-  <td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
+  <td><code>BUILD_TOOLS</code></td>
+  <td>control whether to build LAMMPS tools</td>
   <td>
   <dl>
     <dt><code>off</code> (default)</dt>
@@ -561,23 +585,6 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </dl>
   </td>
 </tr>
-<tr>
-  <td><code>PKG_MEAM</code></td>
-  <td>
-<p>A pair style for the modified embedded atom (MEAM) potential.</p>
-
-<p><strong>Please note that the MEAM package has been superseded by the USER-MEAMC package,
-which is a direct translation of the MEAM package to C++. USER-MEAMC contains
-additional optimizations making it run faster than MEAM on most machines, while
-providing the identical features and USER interface.</strong></p>
-  </td>
-  <td>
-  <dl>
-    <dt><code>off</code> (default)</dt>
-    <dt><code>on</code></dt>
-  </dl>
-  </td>
-</tr>
 <tr>
   <td><code>PKG_MISC</code></td>
   <td>
@@ -634,21 +641,6 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
-<tr>
-  <td><code>PKG_REAX</code></td>
-  <td>
-  A pair style which wraps a Fortran library which implements the ReaxFF
-  potential, which is a universal reactive force field. See the USER-REAXC
-  package for an alternate implementation in C/C++. Also a fix reax/bonds
-  command for monitoring molecules as bonds are created and destroyed.
-  </td>
-  <td>
-  <dl>
-    <dt><code>off</code> (default)</dt>
-    <dt><code>on</code></dt>
-  </dl>
-  </td>
-</tr>
 <tr>
   <td><code>PKG_REPLICA</code></td>
   <td>
@@ -695,6 +687,16 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_SPIN</code></td>
+  <td>Model atomic magnetic spins classically, coupled to atoms moving in the usual manner via MD. Various pair, fix, and compute styles.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_SNAP</code></td>
   <td>
@@ -757,6 +759,16 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_MESSAGE</code></td>
+  <td>Commands to use LAMMPS as either a client or server and couple it to another application.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_MSCG</code></td>
   <td>
@@ -811,6 +823,18 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_VORONOI</code></td>
+  <td>
+  A compute command which calculates the Voronoi tesselation of a collection of atoms by wrapping the Voro++ library. This can be used to calculate the local volume or each atoms or its near neighbors.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -825,6 +849,16 @@ providing the identical features and USER interface.</strong></p>
 </tr>
 </thead>
 <tbody>
+<tr>
+  <td><code>PKG_USER-ADIOS</code></td>
+  <td>ADIOS is a high-performance I/O library. This package implements the dump “atom/adios” and dump “custom/adios” commands to write data using the ADIOS library.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-ATC</code></td>
   <td>
@@ -853,6 +887,18 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-BOCS</code></td>
+  <td>
+  This package provides fix bocs, a modified version of fix npt which includes the pressure correction to the barostat as outlined in: N. J. H. Dunn and W. G. Noid, “Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids,” J. Chem. Phys. 143, 243148 (2015).
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-CGDNA</code></td>
   <td>
@@ -1142,6 +1188,30 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-PLUMED</code></td>
+  <td>
+  The fix plumed command allows you to use the PLUMED free energy plugin for molecular dynamics to analyze and bias your LAMMPS trajectory on the fly. The PLUMED library is called from within the LAMMPS input script by using the <code>fix plumed</code> command.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PKG_USER-PTM</code></td>
+  <td>
+  A <code>compute ptm/atom</code> command that calculates local structure characterization using the Polyhedral Template Matching methodology.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-QTB</code></td>
   <td>
@@ -1197,6 +1267,33 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-SCAFACOS</code></td>
+  <td>
+  A KSpace style which wraps the ScaFaCoS Coulomb solver library to compute long-range Coulombic interactions.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PKG_USER-SDPD</code></td>
+  <td>
+  A pair style for smoothed dissipative particle dynamics (SDPD), which is an
+  extension of smoothed particle hydrodynamics (SPH) to mesoscale where thermal
+  fluctuations are important (see the USER-SPH package). Also two fixes for
+  moving and rigid body integration of SPH/SDPD particles (particles of
+  <code>atom_style meso</code>).</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-SMD</code></td>
   <td>
@@ -1280,6 +1377,23 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-YAFF</code></td>
+  <td>
+  Some potentials that are also implemented in the Yet Another Force Field (YAFF) code.
+  The expressions and their use are discussed in the following papers:
+  <ul>
+    <li><a href="http://dx.doi.org/10.1002/jcc.23877" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015)</a></li>
+    <li><a href="http://dx.doi.org/10.1002/jcc.25173" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018)</a></li>
+  </ul>
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -1300,14 +1414,27 @@ providing the identical features and USER interface.</strong></p>
   <td><code>FFT</code></td>
   <td>
     <p>FFT library for KSPACE package</p>
-    <p>If either MKL or FFTW is selected <code>cmake</code> will try to locate these libraries automatically. To control which one should be used please see the options below for each FFT library.</p>
+    <p>If either MKL or FFTW is selected <code>cmake</code> will try to locate
+    these libraries automatically. To control which one should be used please see
+    the options below for each FFT library.  Otherwise it will default to KISS
+    FFT.</p>
   </td>
   <td>
   <dl>
-    <dt><code>KISS</code></dt>
     <dt><code>FFTW3</code></dt>
     <dt><code>FFTW2</code></dt>
     <dt><code>MKL</code></dt>
+    <dt><code>KISS</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>FFT_SINGLE</code></td>
+  <td>Use single-precision floating-point in FFT</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default = double precision)</dt>
+    <dt><code>on</code></dt>
   </dl>
   </td>
 </tr>
@@ -1325,60 +1452,6 @@ providing the identical features and USER interface.</strong></p>
 </tbody>
 </table>
 
-### MKL
-
-<table>
-<thead>
-<tr>
-  <th>Option</th>
-  <th>Description</th>
-  <th>Values</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-  <td><code>MKL_INCLUDE_DIRS</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-<tr>
-  <td><code>MKL_LIBRARIES</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-</tbody>
-</table>
-
-TODO static vs dynamic linking
-
-### FFTW2
-
-<table>
-<thead>
-<tr>
-  <th>Option</th>
-  <th>Description</th>
-  <th>Values</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-  <td><code>FFTW2_INCLUDE_DIRS</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-<tr>
-  <td><code>FFTW2_LIBRARIES</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-</tbody>
-</table>
-
 ### FFTW3
 
 <table>
@@ -1392,24 +1465,57 @@ TODO static vs dynamic linking
 <tbody>
 <tr>
   <td><code>FFTW3_INCLUDE_DIRS</code></td>
-  <td></td>
+  <td>path to FFTW3 include files</td>
   <td>
   </td>
 </tr>
 <tr>
   <td><code>FFTW3_LIBRARIES</code></td>
-  <td></td>
+  <td>list of paths to FFTW3 libraries</td>
   <td>
   </td>
 </tr>
 </tbody>
 </table>
 
+### MKL
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>MKL_INCLUDE_DIRS</code></td>
+  <td>path to MKL include files</td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>MKL_LIBRARIES</code></td>
+  <td>list of paths to MKL libraries</td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### BLAS
+
+See [FindBLAS documentation](https://cmake.org/cmake/help/latest/module/FindBLAS.html)
+
 ### LAPACK
-TODO
+
+See [FindLAPACK documentation](https://cmake.org/cmake/help/latest/module/FindLAPACK.html)
 
 ### PYTHON Package
 
+See [FindPYTHON documentation](https://cmake.org/cmake/help/latest/module/FindPython.html)
+
 ### USER-INTEL Package
 
 <table>
@@ -1499,10 +1605,11 @@ target API.
   <td>
   <dl>
     <dt><code>sm_20</code> (Fermi)</dt>
-    <dt><code>sm_30</code> (Kepler)</dt>
+    <dt><code>sm_30</code> (Kepler) (default)</dt>
     <dt><code>sm_50</code> (Maxwell)</dt>
     <dt><code>sm_60</code> (Pascal)</dt>
     <dt><code>sm_70</code> (Volta)</dt>
+    <dt><code>sm_75</code> (Turing)</dt>
   </dl>
   </td>
 </tr>
@@ -1534,13 +1641,14 @@ target API.
 </tbody>
 </table>
 
-### VORONOI Package
+### KIM Package
 
-TODO
+Requires installation of the KIM library with API v2
 
-### USER-SMD Package
-
-Requires a Eigen3 installation
+If `DOWNLOAD_KIM` is set, the KIM library will be downloaded and built inside
+the CMake build directory. If the KIM library is already on your system (in a
+location CMake cannot find it), set the `PKG_CONFIG_PATH` environment variable
+so that `libkim-api` can be found.
 
 <table>
 <thead>
@@ -1551,9 +1659,323 @@ Requires a Eigen3 installation
 </tr>
 </thead>
 <tbody>
+<tr>
+  <td><code>DOWNLOAD_KIM</code></td>
+  <td>Download KIM API v2 and compile it as part of the build.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### MESSAGE Package
+
+This package can optionally include support for messaging via sockets, using the open-source [ZeroMQ library](http://zeromq.org/), which must be installed on your system.
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>MESSAGE_ZMQ</code></td>
+  <td>Build with ZeroMQ support</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ZMQ_LIBRARY</code></td>
+  <td>
+    ZMQ library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>ZMG_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing ZMQ installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### MSCG Package
+
+Requires installation of the MSCG library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_MSCG</code></td>
+  <td>Download MSCG and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>MSCG_LIBRARY</code></td>
+  <td>
+    MSCG library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>MSCG_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing MSCG installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### VORONOI Package
+
+Requires installation of the Voro++ library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_VORO</code></td>
+  <td>Download Voro++ and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>VORO_LIBRARY</code></td>
+  <td>
+    Voro++ library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>VORO_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing Voro++ installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-LATTE Package
+
+Requires installation of the LATTE library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_LATTE</code></td>
+  <td>Download LATTE and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LATTE_LIBRARY</code></td>
+  <td>
+    LATTE library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-PLUMED Package
+
+Requires installation of the PLUMED library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_PLUMED</code></td>
+  <td>Download PLUMED and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PLUMED_MODE</code></td>
+  <td>
+    Determines the linkage mode for the PLUMED library.
+  </td>
+  <td>
+  <dl>
+    <dt><code>static</code> (default)</dt>
+    <dt><code>shared</code></dt>
+    <dt><code>runtime</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-LATTE Package
+
+Requires installation of the LATTE library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_LATTE</code></td>
+  <td>Download LATTE and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LATTE_LIBRARY</code></td>
+  <td>
+    LATTE library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-SMD Package
+
+Requires installation of the Eigen3 library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_EIGEN3</code></td>
+  <td>Download Eigen3 and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>EIGEN3_INCLUDE_DIR</code></td>
-  <td></td>
+  <td>
+    Provide include directory of existing Eigen3 installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+
+### USER-SCAFACOS Package
+
+To build with this package, you must download and build the [ScaFaCoS Coulomb solver library](http://www.scafacos.de/)
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_SCAFACOS</code></td>
+  <td>Download SCAFACOS and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>SCAFACOS_LIBRARY</code></td>
+  <td>
+    SCAFACOS library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>SCAFACOS_INCLUDE_DIR</code></td>
+  <td>
+    SCAFACOS include directory (only needed if at custom location)
+  </td>
   <td>
   </td>
 </tr>
@@ -1791,5 +2213,82 @@ cmake -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icpc -D CMAKE_Fortran_COMPIL
 cmake -D CMAKE_C_COMPILER=clang -D CMAKE_CXX_COMPILER=clang++ -D CMAKE_Fortran_COMPILER=flang ../cmake
 ```
 
+## LAMMPS Developer Options
 
-## Examples
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>ENABLE_TESTING</code></td>
+  <td>Control wheather to add tests via CTest</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_TESTING_SOURCE_DIR</code></td>
+  <td>Custom location of lammps-testing repository (optional). If not specified it will download it via Git</td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_TESTING_GIT_TAG</code></td>
+  <td>If lammps-testing repository is cloned, this is the tag/commit that will be checked out</td>
+  <td>
+  <dl>
+    <dt><code>master</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_COVERAGE</code></td>
+  <td>Enables code coverage support via gcov and adds a gcovr build target to generate a coverage report.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_ADDRESS</code></td>
+  <td>Enables Address Sanitizer support when compiling using GCC or Clang for detecting memory leaks in binaries while running them. See https://clang.llvm.org/docs/AddressSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_UNDEFINED</code></td>
+  <td>Enables Undefined Behavior Sanitizer support when compiling using GCC or Clang for detecting code that is running into undefined behavior of the language. See https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_THREAD</code></td>
+  <td>Enables Thread Sanitizer support when compiling using GCC or Clang for detecting data races in binaries while running them. See https://clang.llvm.org/docs/ThreadSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
diff --git a/cmake/etc/profile.d/lammps.csh.in b/cmake/etc/profile.d/lammps.csh.in
index 42f222d67c..1c13583914 100644
--- a/cmake/etc/profile.d/lammps.csh.in
+++ b/cmake/etc/profile.d/lammps.csh.in
@@ -1,4 +1,4 @@
 # set environment for LAMMPS and msi2lmp executables
 # to find potential and force field files
-if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@
-if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_FRC_FILES_DIR@
+if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_INSTALL_DATADIR@/potentials
+if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_INSTALL_DATADIR@/frc_files
diff --git a/cmake/etc/profile.d/lammps.sh.in b/cmake/etc/profile.d/lammps.sh.in
index c1967cb5b2..1542a8982f 100644
--- a/cmake/etc/profile.d/lammps.sh.in
+++ b/cmake/etc/profile.d/lammps.sh.in
@@ -1,5 +1,5 @@
 # set environment for LAMMPS and msi2lmp executables
 # to find potential and force field files
-LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
-MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_FRC_FILES_DIR@}
+LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_INSTALL_DATADIR@/potentials}
+MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_INSTALL_DATADIR@/frc_files}
 export LAMMPS_POTENTIALS MSI2LMP_LIBRARY
diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake
index b53e5a7b93..920b377e48 100644
--- a/cmake/presets/mingw-cross.cmake
+++ b/cmake/presets/mingw-cross.cmake
@@ -3,9 +3,9 @@ set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
                  REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD
                  USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
                  USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD
-                 USER-MEAMC USER-MESO USER-MISC USER-MOFFF USER-MOLFILE USER-OMP
-                 USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD USER-SMD
-                 USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
+                 USER-MEAMC USER-MESO USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE
+                 USER-OMP USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD
+                 USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
 
 foreach(PKG ${WIN_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@@ -14,4 +14,4 @@ endforeach()
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
 set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
-set(INTEL_LRT_MODE "none" CACHE STRING "" FORCE)
+set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer")
diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md
new file mode 100644
index 0000000000..132f2ec4eb
--- /dev/null
+++ b/doc/include-file-conventions.md
@@ -0,0 +1,133 @@
+# Outline of include file conventions in LAMMPS
+
+This purpose of this document is to provide a point of reference
+for LAMMPS developers and contributors as to what include files
+and definitions to put where into LAMMPS source.
+Last change 2019-07-05
+
+## Table of Contents
+
+  * [Motivation](#motivation)
+  * [Rules](#rules)
+  * [Tools](#tools)
+  * [Legacy Code](#legacy-code)
+
+## Motivation
+
+The conventions outlined in this document are supposed to help make
+maintenance of the LAMMPS software easier.  By trying to achieve
+consistency across files contributed by different developers, it will
+become easier for the code maintainers to modify and adjust files and,
+overall, the chance for errors or portability issues will be reduced.
+The rules employed are supposed to minimize naming conflicts and
+simplify dependencies between files and thus speed up compilation. They
+may, as well, make otherwise hidden dependencies visible.
+
+## Rules
+
+Below are the various rules that are applied.  Not all are enforced
+strictly and automatically.  If there are no significant side effects,
+exceptions may be possible for cases where a full compliance to the
+rules may require a large effort compared to the benefit.
+
+### Core Files Versus Package Files
+
+All rules listed below are most strictly observed for core LAMMPS files,
+which are the files that are not part of a package, and the files of the
+packages MOLECULE, MANYBODY, KSPACE, and RIGID.  On the other end of
+the spectrum are USER packages and legacy packages that predate these
+rules and thus may not be fully compliant.  Also, new contributions
+will be checked more closely, while existing code will be incrementally
+adapted to the rules as time and required effort permits.
+
+### System Versus Local Header Files
+
+All system- or library-provided include files are included with angular
+brackets (examples: `#include <cstring>` or `#include <mpi.h>`) while
+include files provided with LAMMPS are included with double quotes
+(examples: `#include "pointers.h"` or `#include "compute_temp.h"`).
+
+For headers declaring functions of the C-library, the corresponding
+C++ versions should be included (examples: `#include <cstdlib>` or
+`#include <cctypes>`).  However, these includes are limited to those defined
+in the C++98 standard.  Some files thus must use the older style until
+the minimum C++ standard requirement of LAMMPS is lifted to C++11 or
+even beyond (examples: `#include <stdint.h>` versus `#include <cstdint>`
+or `#include <inttypes.h>` versus `#include <cinttypes>`).
+
+### C++ Standard Compliance
+
+LAMMPS core files currently correspond to the C++98 standard. Files
+requiring C++11 or later are only permitted in (optional) packages
+and particularly packages that are not part of the list of commonly
+used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID.
+
+Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams.
+Since using both at the same time can cause problems, iostreams should
+be avoided where possible.
+
+### Lean Header Files
+
+Header files will typically contain the definition of a (single) class.
+These header files should have as few include statements as possible.
+This is particularly important for classes that implement a "style" and
+thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
+all be included in the auto-generated `"some_style.h"` files which 
+results in a high potential for direct or indirect symbol name clashes.
+
+In the ideal case, the header would only include one file defining the
+parent class. That would typically be either `#include "pointers.h"` for
+the `Pointers` class, or a header of a class derived from it like
+`#include "pair.h"` for the `Pair` class and so on.  References to other
+classes inside the class should be make through pointers, for which forward
+declarations (inside the `LAMMPS_NS` or the new class' namespace) can
+be employed.  The full definition will then be included into the corresponding
+implementation file.  In the given example from above, the header file
+would be called `some_name.h` and the implementation `some_name.cpp` (all
+lower case with underscores, while the class itself would be in camel case
+and no underscores `SomeName`, and the style name with lower case names separated by
+a forward slash).
+
+### Implementation Files
+
+In the implementation files (typically, those would have the same base name
+as the corresponding header with a .cpp extension instead of .h) include
+statements should follow the "include what you use" principle.
+
+### Order of Include Statements
+
+Include files should be included in this order:
+* the header matching the implementation (`some_class.h` for file `some_class.cpp`)
+* mpi.h
+* system and library headers (anything that is using angular brackets; C-library headers first, then C++)
+* LAMMPS local headers (preferably in alphabetical order)
+
+### Special Cases and Exceptions
+
+#### pointers.h
+
+The `pointer.h` header file also includes `cstdio` and `lmptype.h`
+(and through it `stdint.h`, `intttypes.h`, cstdlib, and `climits`).
+This means any header including `pointers.h` can assume that `FILE`,
+`NULL`, `INT_MAX` are defined.
+
+## Tools
+
+The [Include What You Use tool](https://include-what-you-use.org/)
+can be used to provide supporting information about compliance with
+the rules listed here.  There are some limitations and the IWYU tool
+may give incorrect advice.  The tools is activated by setting the
+CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the
+path of the `include-what-you-use` command.  When activated, the
+tool will be run after each compilation and provide suggestions for
+which include files should be added or removed.
+
+## Legacy Code
+
+A lot of code predates the application of the rules in this document
+and the rules themselves are a moving target.  So there are going to be
+significant chunks of code that do not fully comply.  This applies
+for example to the USER-REAXC, or the USER-ATC package.  The LAMMPS
+developers are dedicated to make an effort to improve the compliance
+and welcome volunteers wanting to help with the process.
+
diff --git a/doc/lammps.1 b/doc/lammps.1
index 4685ad22a3..ac19749dd6 100644
--- a/doc/lammps.1
+++ b/doc/lammps.1
@@ -1,4 +1,4 @@
-.TH LAMMPS "19 July 2019" "2019-07-19"
+.TH LAMMPS "7 August 2019" "2019-08-07"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
diff --git a/doc/src/Build.txt b/doc/src/Build.txt
index df30af36f5..8906549350 100644
--- a/doc/src/Build.txt
+++ b/doc/src/Build.txt
@@ -29,6 +29,7 @@ as described on the "Install"_Install.html doc page.
    Build_package
    Build_extras
    Build_windows
+   Build_development
 
 END_RST -->
 
@@ -41,7 +42,8 @@ END_RST -->
 "Optional build settings"_Build_settings.html
 "Include packages in build"_Build_package.html
 "Packages with extra build options"_Build_extras.html
-"Notes for building LAMMPS on Windows"_Build_windows.html  :all(b)
+"Notes for building LAMMPS on Windows"_Build_windows.html
+"Development build options (CMake only)"_Build_development.html  :all(b)
 
 If you have problems building LAMMPS, it is often due to software
 issues on your local machine.  If you can, find a local expert to
diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt
index fa4ef12586..04e11009af 100644
--- a/doc/src/Build_basics.txt
+++ b/doc/src/Build_basics.txt
@@ -235,12 +235,16 @@ running LAMMPS from Python via its library interface.
 
 -D BUILD_EXE=value           # yes (default) or no
 -D BUILD_LIB=value           # yes or no (default)
--D BUILD_SHARED_LIBS=value   # yes or no (default) :pre
+-D BUILD_SHARED_LIBS=value   # yes or no (default)
+-D LAMMPS_LIB_SUFFIX=name    # name = mpi, serial, mybox, titan, laptop, etc
+                             # no default value :pre
+
 
 Setting BUILD_EXE=no will not produce an executable.  Setting
 BUILD_LIB=yes will produce a static library named liblammps.a.
 Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a
-shared library named liblammps.so.
+shared library named liblammps.so. If LAMMPS_LIB_SUFFIX is set the generated
+libraries will be named liblammps_name.a or liblammps_name.so instead.
 
 [Traditional make]:
 
@@ -310,6 +314,30 @@ current LAMMPS version (HTML and PDF files), from the website
 
 :line
 
+Build LAMMPS tools :h4,link(tools)
+
+Some tools described in "Auxiliary tools"_Tools.html can be built directly
+using CMake or Make.
+
+[CMake variable]:
+
+-D BUILD_TOOLS=value       # yes or no (default) :pre
+
+The generated binaries will also become part of the LAMMPS installation (see below)
+
+[Traditional make]:
+
+cd lammps/tools
+make all              # build all binaries of tools
+make binary2txt       # build only binary2txt tool
+make chain            # build only chain tool
+make micelle2d        # build only micelle2d tool
+make thermo_extract   # build only thermo_extract tool
+:pre
+
+:line
+
+
 Install LAMMPS after a build :h4,link(install)
 
 After building LAMMPS, you may wish to copy the LAMMPS executable of
diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt
index a16ba995a8..b2411272eb 100644
--- a/doc/src/Build_cmake.txt
+++ b/doc/src/Build_cmake.txt
@@ -52,11 +52,17 @@ LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
 ccache (= Compiler Cache) software may speed up repeated compilation
 even more.
 
-After compilation, you can optionally copy the LAMMPS executable and
-library into your system folders (by default under $HOME/.local) with:
+After compilation, you may optionally install the LAMMPS executable into
+your system with:
 
 make install    # optional, copy LAMMPS executable & library elsewhere :pre
 
+This will install the lammps executable and library (if requested), some
+tools (if configured) and additional files like library API headers,
+manpages, potential and force field files. The location of the installation
+tree is set by the CMake variable "CMAKE_INSTALL_PREFIX" which defaults
+to $\{HOME\}/.local
+
 :line
 
 There are 3 variants of CMake: a command-line version (cmake), a text mode
@@ -114,7 +120,7 @@ The argument can be preceeded or followed by various CMake
 command-line options.  Several useful ones are:
 
 -D CMAKE_INSTALL_PREFIX=path  # where to install LAMMPS executable/lib if desired
--D CMAKE_BUILD_TYPE=type      # type = Release or Debug
+-D CMAKE_BUILD_TYPE=type      # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
 -G output                     # style of output CMake generates
 -DVARIABLE=value              # setting for a LAMMPS feature to enable
 -D VARIABLE=value             # ditto, but cannot come after CMakeLists.txt dir
diff --git a/doc/src/Build_development.txt b/doc/src/Build_development.txt
new file mode 100644
index 0000000000..16a3d3d20e
--- /dev/null
+++ b/doc/src/Build_development.txt
@@ -0,0 +1,86 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Development build options (CMake only) :h3
+
+The CMake build of LAMMPS has a few extra options which are useful during
+development,  testing or debugging.
+
+:line
+
+Verify compilation flags :h4,link(compilation)
+
+Sometimes it is necessary to verify the complete sequence of compilation flags
+generated by the CMake build. To enable a more verbose output during
+compilation you can use the following option.
+
+-D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes :pre
+
+Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
+
+make VERBOSE=1 :pre
+
+:line
+
+Address, Undefined Behavior, and Thread Sanitizer Support :h4,link(sanitizer)
+
+Compilers such as GCC and Clang support generating binaries which use different
+sanitizers to detect problems in code during run-time. They can detect "memory leaks"_https://clang.llvm.org/docs/AddressSanitizer.html,
+code that runs into "undefined behavior"_https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html of the
+language and "data races"_https://clang.llvm.org/docs/ThreadSanitizer.html in threaded code.
+
+The following settings allow you enable these features if your compiler supports
+it. Please note that they come with a performance hit. However, they are
+usually faster than using tools like Valgrind.
+
+-D ENABLE_SANITIZE_ADDRESS=value    # enable Address Sanitizer, value = no (default) or yes
+-D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behaviour Sanitizer, value = no (default) or yes
+-D ENABLE_SANITIZE_THREAD=value     # enable Thread Sanitizer, value = no (default) or yes
+:pre
+
+:line
+
+Code Coverage and Testing :h4,link(testing)
+
+We do extensive regression testing of the LAMMPS code base on a continuous
+basis. Some of the logic to do this has been added to the CMake build so
+developers can run the tests directly on their workstation. 
+
+NOTE: this is incomplete and only represents a small subset of tests that we run
+
+-D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes
+-D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)
+-D LAMMPS_TESTING_GIT_TAG=value       # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
+:pre
+
+If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
+
+make test
+:pre
+
+The test cases used come from the lammps-testing repository. They are
+derivatives of the examples folder with some modifications to make the run
+faster.
+
+You can also collect code coverage metrics while running the tests by enabling
+coverage support during building.
+
+-D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes :pre
+
+This will also add the following targets to generate coverage reports after running the LAMMPS executable:
+
+make test               # run tests first!
+make gen_coverage_html  # generate coverage report in HTML format
+make gen_coverage_xml   # generate coverage report in XML format
+:pre
+
+These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
+
+pip install git+https://github.com/gcovr/gcovr.git :pre
+:pre
diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt
index 3fc23c5618..b0bf0c9cd6 100644
--- a/doc/src/Build_extras.txt
+++ b/doc/src/Build_extras.txt
@@ -88,7 +88,7 @@ which GPU hardware to build for.
                           # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
 -D GPU_ARCH=value         # primary GPU hardware choice for GPU_API=cuda
                           # value = sm_XX, see below
-                          # default is Cuda-compiler dependent, but typically sm_20
+                          # default is sm_30
 -D CUDPP_OPT=value        # optimization setting for GPU_API=cuda
                           # enables CUDA Performance Primitives Optimizations
                           # value = yes (default) or no
@@ -172,22 +172,17 @@ KIM package :h4,link(kim)
 
 To build with this package, the KIM library with API v2 must be downloaded
 and built on your system.  It must include the KIM models that you want to
-use with LAMMPS. If you want to use the "kim_query"_kim_query.html
+use with LAMMPS. If you want to use the "kim_query"_kim_commands.html
 command, you also need to have libcurl installed with the matching
 development headers and the curl-config tool.
 
-Note that in LAMMPS lingo, a KIM model driver is a pair style
-(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
-element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file.  Also note that downloading and installing
-the KIM API library with all its models, may take a long time (10s of
-minutes to hours) to build.  Of course you only need to do that once.
+See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to
+learn how to install a pre-build binary of the OpenKIM Repository of Models.
+See the list of all KIM models here: https://openkim.org/browse/models
 
-See the list of KIM model drivers here:
-https://openkim.org/browse/model-drivers/alphabetical
-
-See the list of all KIM models here:
-https://openkim.org/browse/models/by-model-drivers
+(Also note that when downloading and installing from source
+the KIM API library with all its models, may take a long time (tens of
+minutes to hours) to build.  Of course you only need to do that once.)
 
 [CMake build]:
 
@@ -359,6 +354,9 @@ be installed on your system.
 [CMake build]:
 
 -D MESSAGE_ZMQ=value    # build with ZeroMQ support, value = no (default) or yes
+-D ZMQ_LIBRARY=path     # ZMQ library file (only needed if a custom location)
+-D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location)
+:pre
 
 [Traditional make]:
 
@@ -371,6 +369,7 @@ simply invoke the lib/message/Install.py script with the specified args:
 make lib-message               # print help message
 make lib-message args="-m -z"  # build with MPI and socket (ZMQ) support
 make lib-message args="-s"     # build as serial lib with no ZMQ support
+:pre
 
 The build should produce two files: lib/message/cslib/src/libmessage.a
 and lib/message/Makefile.lammps.  The latter is copied from an
diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt
index 80f91d5291..d0d7657c07 100644
--- a/doc/src/Commands_all.txt
+++ b/doc/src/Commands_all.txt
@@ -68,7 +68,9 @@ An alphabetic list of all general LAMMPS commands.
 "improper_style"_improper_style.html,
 "include"_include.html,
 "jump"_jump.html,
-"kim_query"_kim_query.html,
+"kim_init"_kim_commands.html,
+"kim_interactions"_kim_commands.html,
+"kim_query"_kim_commands.html,
 "kspace_modify"_kspace_modify.html,
 "kspace_style"_kspace_style.html,
 "label"_label.html,
diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt
index f566702609..e035eb8431 100644
--- a/doc/src/Commands_compute.txt
+++ b/doc/src/Commands_compute.txt
@@ -66,6 +66,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "group/group"_compute_group_group.html,
 "gyration"_compute_gyration.html,
 "gyration/chunk"_compute_gyration_chunk.html,
+"gyration/shape"_compute_gyration_shape.html,
 "heat/flux"_compute_heat_flux.html,
 "heat/flux/tally"_compute_tally.html,
 "hexorder/atom"_compute_hexorder_atom.html,
@@ -80,6 +81,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "meso/e/atom"_compute_meso_e_atom.html,
 "meso/rho/atom"_compute_meso_rho_atom.html,
 "meso/t/atom"_compute_meso_t_atom.html,
+"momentum"_compute_momentum.html,
 "msd"_compute_msd.html,
 "msd/chunk"_compute_msd_chunk.html,
 "msd/nongauss"_compute_msd_nongauss.html,
diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt
index d2d781d4b2..cfd2bcf2ef 100644
--- a/doc/src/Commands_fix.txt
+++ b/doc/src/Commands_fix.txt
@@ -232,6 +232,7 @@ OPT.
 "wall/lj1043"_fix_wall.html,
 "wall/lj126"_fix_wall.html,
 "wall/lj93 (k)"_fix_wall.html,
+"wall/morse"_fix_wall.html,
 "wall/piston"_fix_wall_piston.html,
 "wall/reflect (k)"_fix_wall_reflect.html,
 "wall/region"_fix_wall_region.html,
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
index 6077fad8ec..47d4c40d8e 100644
--- a/doc/src/Commands_pair.txt
+++ b/doc/src/Commands_pair.txt
@@ -65,6 +65,7 @@ OPT.
 "colloid (go)"_pair_colloid.html,
 "comb (o)"_pair_comb.html,
 "comb3"_pair_comb.html,
+"cosine/squared"_pair_cosine_squared.html,
 "coul/cut (gko)"_pair_coul.html,
 "coul/cut/soft (o)"_pair_fep_soft.html,
 "coul/debye (gko)"_pair_coul.html,
diff --git a/doc/src/Eqs/compute_shape_parameters.jpg b/doc/src/Eqs/compute_shape_parameters.jpg
new file mode 100644
index 0000000000..9e2374561b
Binary files /dev/null and b/doc/src/Eqs/compute_shape_parameters.jpg differ
diff --git a/doc/src/Eqs/compute_shape_parameters.tex b/doc/src/Eqs/compute_shape_parameters.tex
new file mode 100644
index 0000000000..8298efc6e0
--- /dev/null
+++ b/doc/src/Eqs/compute_shape_parameters.tex
@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+ c = l_z - 0.5(l_y+l_x) \\
+ b = l_y - l_x \\
+ k = \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} 
+\end{eqnarray*}
+
+\end{document}
+
diff --git a/doc/src/Eqs/pair_cosine_squared.jpg b/doc/src/Eqs/pair_cosine_squared.jpg
new file mode 100644
index 0000000000..682800652d
Binary files /dev/null and b/doc/src/Eqs/pair_cosine_squared.jpg differ
diff --git a/doc/src/Eqs/pair_cosine_squared.tex b/doc/src/Eqs/pair_cosine_squared.tex
new file mode 100644
index 0000000000..96ac6a305e
--- /dev/null
+++ b/doc/src/Eqs/pair_cosine_squared.tex
@@ -0,0 +1,16 @@
+\documentclass[12pt]{article}
+
+\usepackage{amsmath}
+
+\begin{document}
+
+\begin{align*}
+E = 
+\begin{cases}
+-\epsilon& \quad r < \sigma \\
+-\epsilon\cos\left(\frac{\pi\left(r - \sigma\right)}{2\left(r_c - \sigma\right)}\right)&\quad \sigma \leq r < r_c \\
+0& \quad r \geq r_c
+\end{cases}
+\end{align*}
+
+\end{document}
diff --git a/doc/src/Eqs/pair_cosine_squared_wca.jpg b/doc/src/Eqs/pair_cosine_squared_wca.jpg
new file mode 100644
index 0000000000..086bc63673
Binary files /dev/null and b/doc/src/Eqs/pair_cosine_squared_wca.jpg differ
diff --git a/doc/src/Eqs/pair_cosine_squared_wca.tex b/doc/src/Eqs/pair_cosine_squared_wca.tex
new file mode 100644
index 0000000000..c086be9306
--- /dev/null
+++ b/doc/src/Eqs/pair_cosine_squared_wca.tex
@@ -0,0 +1,11 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - 
+                       2\left(\frac{\sigma}{r}\right)^6 + 1\right]
+                       , \quad r < \sigma
+$$
+
+\end{document}
diff --git a/doc/src/Eqs/pair_kolmogorov_crespi_full.jpg b/doc/src/Eqs/pair_kolmogorov_crespi_full.jpg
index e9d306d505..7ac14f3d0b 100644
Binary files a/doc/src/Eqs/pair_kolmogorov_crespi_full.jpg and b/doc/src/Eqs/pair_kolmogorov_crespi_full.jpg differ
diff --git a/doc/src/Eqs/pair_kolmogorov_crespi_full.tex b/doc/src/Eqs/pair_kolmogorov_crespi_full.tex
index 606aa8b5fe..16bbc25abf 100644
--- a/doc/src/Eqs/pair_kolmogorov_crespi_full.tex
+++ b/doc/src/Eqs/pair_kolmogorov_crespi_full.tex
@@ -27,7 +27,7 @@
   V_{ij} & = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \right ] \\
   \rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\[15pt]
   \rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot  {\bf n}_{j})^2 \\[15pt]
-  f(\rho) & = &  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { \rho/\delta }^{2n}
+  f(\rho) & = &  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n}
 \end{eqnarray*}
 \endgroup
 \end{document}
diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt
index c55d3743ab..c131b10ec6 100644
--- a/doc/src/Errors_messages.txt
+++ b/doc/src/Errors_messages.txt
@@ -2438,6 +2438,14 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
+{Compute gyration ID does not exist for compute gyration/shape} :dt
+
+Self-explanatory. Provide a valid compute ID. :dd
+
+{Compute gyration/shape compute ID does not point to a gyration compute} :dt
+
+Self-explanatory. Provide and ID of a compute gyration command. :dd
+
 {Compute ID for compute reduce does not exist} :dt
 
 Self-explanatory. :dd
@@ -5777,6 +5785,16 @@ definitions. :dd
 
 The data file header lists improper but no improper types. :dd
 
+{Incompatible KIM Simulator Model} :dt
+
+The requested KIM Simulator Model was defined for a different MD code
+and thus is not compatible with LAMMPS. :dd
+
+{Incompatible units for KIM Simulator Model} :dt
+
+The selected unit style is not compatible with the requested KIM
+Simulator Model. :dd
+
 {Incomplete use of variables in create_atoms command} :dt
 
 The var and set options must be used together. :dd
@@ -7047,6 +7065,12 @@ The atom style defined does not have this attribute. :dd
 
 The atom style defined does not have these attributes. :dd
 
+{KIM Simulator Model has no Model definition} :dt
+
+There is no model definition (key: model-defn) in the KIM Simulator
+Model.  Please contact the OpenKIM database maintainers to verify
+and potentially correct this. :dd
+
 {KOKKOS package does not yet support comm_style tiled} :dt
 
 Self-explanatory. :dd
@@ -7551,6 +7575,18 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
+{Must use 'kim_style init' command before simulation box is defined} :dt
+
+Self-explanatory. :dd
+
+{Must use 'kim_style define' command after simulation box is defined} :dt
+
+Self-explanatory. :dd
+
+{Must use 'kim_style init' command before 'kim_style define'} :dt
+
+Self-explanatory. :dd
+
 {Must use 'kspace_modify pressure/scalar no' for rRESPA with kspace_style MSM} :dt
 
 The kspace scalar pressure option cannot (yet) be used with rRESPA. :dd
@@ -9494,6 +9530,11 @@ See the "read_data extra/special/per/atom" command
 for info on how to leave space in the special bonds
 list to allow for additional bonds to be formed. :dd
 
+{Species XXX is not supported by this KIM Simulator Model} :dt
+
+The kim_style define command was referencing a species that is not
+present in the requested KIM Simulator Model. :dd
+
 {Specified processors != physical processors} :dt
 
 The 3d grid of processors defined by the processors command does not
diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt
index 1507d6b22c..9f346ba8c1 100644
--- a/doc/src/Errors_warnings.txt
+++ b/doc/src/Errors_warnings.txt
@@ -129,6 +129,16 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
+{Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost} :dt
+
+The communication cutoff defaults to the maximum of what is inferred from
+pair and bond styles (will be zero, if none are defined) and what is specified
+via "comm_modify cutoff"_comm_modify.html (defaults to 0.0).  If this results
+to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use
+incorrect periodic images of atoms in interaction lists.  To avoid, either use
+"pair style zero"_pair_zero.html with a suitable cutoff or use "comm_modify
+cutoff"_comm_modify.html. :dd
+
 {Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt
 
 Self-explanatory. :dd
diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt
index fcf01de383..36d0ac86f9 100644
--- a/doc/src/Examples.txt
+++ b/doc/src/Examples.txt
@@ -73,7 +73,7 @@ granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
 hyper:    global and local hyperdynamics of diffusion on Pt surface
 indent:   spherical indenter into a 2d solid
-kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
+kim:      use of potentials from the "OpenKIM Repository"_openkim
 latte:    examples for using fix latte for DFTB via the LATTE library
 meam:     MEAM test for SiC and shear (same as shear examples)
 melt:     rapid melt of 3d LJ system
@@ -153,3 +153,5 @@ illustrate how to use the command(s) provided in that package.  Many
 of the sub-directories have their own README files which give further
 instructions.  See the "Packages_details"_Packages_details.html doc
 page for more info on specific USER packages.
+
+:link(openkim,https://openkim.org)
diff --git a/doc/src/Howto_chunk.txt b/doc/src/Howto_chunk.txt
index e29cf13167..ef9b49f87c 100644
--- a/doc/src/Howto_chunk.txt
+++ b/doc/src/Howto_chunk.txt
@@ -136,7 +136,9 @@ The "compute chunk/spread/atom"_compute_chunk_spread_atom.html command
 spreads per-chunk values to each atom in the chunk, producing per-atom
 values as its output.  This can be useful for outputting per-chunk
 values to a per-atom "dump file"_dump.html.  Or for using an atom's
-associated chunk value in an "atom-style variable"_variable.html.
+associated chunk value in an "atom-style variable"_variable.html.  Or
+as input to the "fix ave/chunk"_fix_ave_chunk.html command to
+spatially average per-chunk values calculated by a per-chunk compute.
 
 The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a
 peratom value across the atoms in each chunk to produce a value per
@@ -184,12 +186,20 @@ compute cc1 all chunk/atom c_cluster compress yes
 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 :pre
 
-(6) An example of 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 "compute
 chunk/spread/atom"_compute_chunk_spread_atom.html command doc page.
 
-(7) An example of 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 2nd set of micelle-scale chunks (clustered
 molecules, due to hydrophobicity), is explained on the "compute
 chunk/reduce"_compute_reduce_chunk.html command doc page.
+
+(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 "fix ave/chunk"_fix_ave_chunk.html command to calculate an
+average dipole moment vector for each bin.  This example is explained
+on the "compute chunk/spread/atom"_compute_chunk_spread_atom.html
+command doc page.
diff --git a/doc/src/Howto_walls.txt b/doc/src/Howto_walls.txt
index 7522118582..4e4f0c5d6f 100644
--- a/doc/src/Howto_walls.txt
+++ b/doc/src/Howto_walls.txt
@@ -59,14 +59,15 @@ granular particles; all the other commands create smooth walls.
 "fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential
 "fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential
 "fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential
+"fix wall/morse"_fix_wall.html - flat walls, with Morse potential
 "fix wall/region"_fix_wall_region.html - use region surface as wall
 "fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul
 
-The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the
-flat walls to move with a constant velocity, or oscillate in time.
-The "fix wall/region"_fix_wall_region.html command offers the most
-generality, since the region surface is treated as a wall, and the
-geometry of the region can be a simple primitive volume (e.g. a
+The {lj93}, {lj126}, {colloid}, {harmonic}, and {morse} styles all
+allow the flat walls to move with a constant velocity, or oscillate in
+time.  The "fix wall/region"_fix_wall_region.html command offers the
+most generality, since the region surface is treated as a wall, and
+the geometry of the region can be a simple primitive volume (e.g. a
 sphere, or cube, or plane), or a complex volume made from the union
 and intersection of primitive volumes.  "Regions"_region.html can also
 specify a volume "interior" or "exterior" to the specified primitive
diff --git a/doc/src/Install_mac.txt b/doc/src/Install_mac.txt
index 3ab119522c..773c9ec93a 100644
--- a/doc/src/Install_mac.txt
+++ b/doc/src/Install_mac.txt
@@ -10,47 +10,34 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 Download an executable for Mac :h3
 
 LAMMPS can be downloaded, built, and configured for OS X on a Mac with
-"Homebrew"_homebrew.  Only four of the LAMMPS packages are unavailable
-at this time because of additional needs not yet met: KIM, GPU,
-USER-INTEL, USER-ATC.
+"Homebrew"_homebrew.  The following LAMMPS packages are unavailable at this
+time because of additional needs not yet met: GPU, KOKKOS, LATTE, MSCG,
+MESSAGE, MPIIO POEMS VORONOI.
 
 After installing Homebrew, you can install LAMMPS on your system with
 the following commands:
 
-% brew tap homebrew/science
-% brew install lammps              # serial version
-% brew install lammps --with-mpi   # mpi support :pre
+% brew install lammps :pre
 
-This will install the executable "lammps", a python module named
-"lammps", and additional resources with all the standard packages.  To
-get the location of the additional resources type this:
-
-% brew info lammps :pre
-
-This command also tells you additional installation options available.
-The user-packages are available as options, just install them like
-this example for the USER-OMP package:
-
-% brew install lammps --enable-user-omp :pre
-
-It is usually best to install LAMMPS with the most up to date source
-files, which can be done with the "--HEAD" option:
-
-% brew install lammps --HEAD :pre
-
-To re-install the LAMMPS HEAD, run this command occasionally (make sure
-to use the desired options).
-
-% brew install --force lammps --HEAD $\{options\} :pre
+This will install the executables "lammps_serial" and "lammps_mpi", as well as
+the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories.
 
 Once LAMMPS is installed, you can test the installation with the
 Lennard-Jones benchmark file:
 
 % brew test lammps -v :pre
 
+The LAMMPS binary is built with the "KIM package"_Build_extras#kim which
+results in Homebrew also installing the `kim-api` binaries when LAMMPS is
+installed.  In order to use potentials from "openkim.org"_openkim, you can
+install the `openkim-models` package
+
+% brew install openkim-models :pre
+
 If you have problems with the installation you can post issues to
 "this link"_homebrew.
 
 Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
 up the Homebrew capability.
-:link(homebrew,https://github.com/Homebrew/homebrew-science/issues)
+:link(homebrew,https://github.com/Homebrew/homebrew-core/issues)
+:link(openkim,https://openkim.org)
diff --git a/doc/src/Intro_features.txt b/doc/src/Intro_features.txt
index 629e8210b7..d133fd8064 100644
--- a/doc/src/Intro_features.txt
+++ b/doc/src/Intro_features.txt
@@ -92,8 +92,8 @@ commands)
   implicit solvent potentials: hydrodynamic lubrication, Debye
   force-field compatibility with common CHARMM, AMBER, DREIDING, \
     OPLS, GROMACS, COMPASS options
-  access to "KIM archive"_http://openkim.org of potentials via \
-    "pair kim"_pair_kim.html
+  access to the "OpenKIM Repository"_http://openkim.org of potentials via \
+    "kim_init, kim_interactions, and kim_query"_kim_commands.html commands
   hybrid potentials: multiple pair, bond, angle, dihedral, improper \
     potentials can be used in one simulation
   overlaid potentials: superposition of multiple pair potentials :ul
diff --git a/doc/src/JPG/pair_cosine_squared_graphs.jpg b/doc/src/JPG/pair_cosine_squared_graphs.jpg
new file mode 100644
index 0000000000..43559d7ca0
Binary files /dev/null and b/doc/src/JPG/pair_cosine_squared_graphs.jpg differ
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 80d72aac57..c63137ef6f 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="19 Jul 2019 version">
+<META NAME="docnumber" CONTENT="7 Aug 2019 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-19 Jul 2019 version :c,h2
+7 Aug 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 
diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf
index 6194424212..14deceeb87 100644
Binary files a/doc/src/PDF/colvars-refman-lammps.pdf and b/doc/src/PDF/colvars-refman-lammps.pdf differ
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index bd5addda6f..eead133add 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -338,22 +338,37 @@ KIM package :link(PKG-KIM),h4
 
 [Contents:]
 
-A "pair_style kim"_pair_kim.html command which is a wrapper on the
-Knowledge Base for Interatomic Models (KIM) repository of interatomic
-potentials, enabling any of them to be used in LAMMPS simulations.
-Also a "kim_query"_kim_query.html command, which allows to query
-the OpenKIM database for stored properties.
+This package contains a set of commands that serve as a wrapper on the
+"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org
+repository of interatomic models (IMs)
+enabling compatible ones to be used in LAMMPS simulations.
+This includes "kim_init and kim_interactions"_kim_commands.html
+commands to select, initialize and instantiate the IM, and a
+"kim_query"_kim_commands.html command to perform web queries
+for material property predictions of OpenKIM IMs.
+Support for KIM IMs that conform to the
+"KIM Application Programming Interface (API)"_https://openkim.org/kim-api/
+is provided by the "pair_style kim"_pair_kim.html command.
 
-To use this package you must have the KIM library available on your
-system.
+NOTE: The command {pair_style kim} is called by {kim_interactions} and
+is not recommended to be directly used in input scripts.
+
+To use this package you must have the KIM API library available on your
+system. The KIM API is available for download on the
+"OpenKIM website"_https://openkim.org/kim-api/.
+When installing LAMMPS from binary, the kim-api package
+is a dependency that is automatically downloaded and installed.
 
 Information about the KIM project can be found at its website:
-https://openkim.org.  The KIM project is led by Ellad Tadmor and Ryan
-Elliott (U Minnesota).
+"https://openkim.org"_https://openkim.org.
+The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota)
+and is funded by the "National Science Foundation"_https://www.nsf.gov/.
 
 [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
-API which the "pair_style kim"_pair_kim.html command uses.  He
-developed the pair style.
+API and the {pair_style kim} command. Axel Kohlmeyer (Temple U) and
+Ellad Tadmor (U Minnesota) contributed to the "kim_commands"_kim_commands.html
+interface in close collaboration with Ryan Elliott.
+
 
 [Install:]
 
@@ -363,10 +378,11 @@ extras"_Build_extras.html doc page.
 
 [Supporting info:]
 
+"kim_commands"_kim_commands.html
+"pair_style kim"_pair_kim.html
 src/KIM: filenames -> commands
 src/KIM/README
 lib/kim/README
-"pair_style kim"_pair_kim.html
 examples/kim :ul
 
 :line
@@ -984,9 +1000,9 @@ USER-ADIOS package :link(PKG-USER-ADIOS),h4
 
 [Contents:]
 
-ADIOS is a high-performance I/O library. This package implements the 
+ADIOS is a high-performance I/O library. This package implements the
 dump "atom/adios" and dump "custom/adios" commands to write data using
-the ADIOS library. 
+the ADIOS library.
 
 [Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team.
 
@@ -1175,7 +1191,7 @@ USER-PLUMED package :link(PKG-USER-PLUMED),h4
 The fix plumed command allows you to use the PLUMED free energy plugin
 for molecular dynamics to analyze and bias your LAMMPS trajectory on
 the fly.  The PLUMED library is called from within the LAMMPS input
-script by using the "fix plumed _fix_plumed.html command.
+script by using the "fix plumed"_fix_plumed.html command.
 
 [Authors:] The "PLUMED library"_#PLUMED is written and maintained by
 Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth
diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt
index 87b272a866..df1a57421a 100644
--- a/doc/src/Run_options.txt
+++ b/doc/src/Run_options.txt
@@ -126,9 +126,10 @@ are intended for computational work like running LAMMPS.  By default
 Ng = 1 and Ns is not set.
 
 Depending on which flavor of MPI you are running, LAMMPS will look for
-one of these 3 environment variables
+one of these 4 environment variables
 
 SLURM_LOCALID (various MPI variants compiled with SLURM support)
+MPT_LRANK (HPE MPI)
 MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
 OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) :pre
 
diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt
index 482259142b..9a792f6cc6 100644
--- a/doc/src/comm_modify.txt
+++ b/doc/src/comm_modify.txt
@@ -40,11 +40,12 @@ coordinates and other properties are exchanged between neighboring
 processors and stored as properties of ghost atoms.
 
 NOTE: These options apply to the currently defined comm style.  When
-you specify a "comm_style"_comm_style.html command, all communication
-settings are restored to their default values, including those
+you specify a "comm_style"_comm_style.html or
+"read_restart"_read_restart.html command, all communication settings
+are restored to their default or stored values, including those
 previously reset by a comm_modify command.  Thus if your input script
-specifies a comm_style command, you should use the comm_modify command
-after it.
+specifies a comm_style or read_restart command, you should use the
+comm_modify command after it.
 
 The {mode} keyword determines whether a single or multiple cutoff
 distances are used to determine which atoms to communicate.
@@ -69,9 +70,15 @@ processors.  By default the ghost cutoff = neighbor cutoff = pairwise
 force cutoff + neighbor skin.  See the "neighbor"_neighbor.html command
 for more information about the skin distance.  If the specified Rcut is
 greater than the neighbor cutoff, then extra ghost atoms will be acquired.
-If the provided cutoff is smaller, the provided value will be ignored
-and the ghost cutoff is set to the neighbor cutoff. Specifying a
-cutoff value of 0.0 will reset any previous value to the default.
+If the provided cutoff is smaller, the provided value will be ignored,
+the ghost cutoff is set to the neighbor cutoff and a warning will be
+printed. Specifying a cutoff value of 0.0 will reset any previous value
+to the default. If bonded interactions exist and equilibrium bond length
+information is available, then also a heuristic based on that bond length
+is computed. It is used as communication cutoff, if there is no pair
+style present and no {comm_modify cutoff} command used. Otherwise a
+warning is printed, if this bond based estimate is larger than the
+communication cutoff used. A
 
 The {cutoff/multi} option is equivalent to {cutoff}, but applies to
 communication mode {multi} instead. Since in this case the communication
diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt
index cf716df9ac..a5c9b568ed 100644
--- a/doc/src/commands_list.txt
+++ b/doc/src/commands_list.txt
@@ -53,7 +53,7 @@ Commands :h1
    include
    info
    jump
-   kim_query
+   kim_commands
    kspace_modify
    kspace_style
    label
diff --git a/doc/src/compute.txt b/doc/src/compute.txt
index 53ed373aa5..214fbdefc4 100644
--- a/doc/src/compute.txt
+++ b/doc/src/compute.txt
@@ -177,7 +177,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "angle"_compute_angle.html - energy of each angle sub-style
 "angle/local"_compute_angle_local.html - theta and energy of each angle
 "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
-"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed “c” lattice vector of each atom
+"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed "c" lattice vector of each atom
 "body/local"_compute_body_local.html - attributes of body sub-particles
 "bond"_compute_bond.html - energy of each bond sub-style
 "bond/local"_compute_bond_local.html - distance and energy of each bond
@@ -213,9 +213,11 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "group/group"_compute_group_group.html - energy/force between two groups of atoms
 "gyration"_compute_gyration.html - radius of gyration of group of atoms
 "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk
+"gyration/shape"_compute_gyration_shape.html - compute shape parameters from radius of gyration tensor
 "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
 "heat/flux/tally"_compute_tally.html -
 "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
+"hma"_compute_hma.html - harmonically mapped averaging for atomic crystals
 "improper"_compute_improper.html - energy of each improper sub-style
 "improper/local"_compute_improper_local.html - angle of each improper
 "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
@@ -227,6 +229,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
 "meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms
 "meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
+"momentum"_compute_momentum.html - translational momentum
 "msd"_compute_msd.html - mean-squared displacement of group of atoms
 "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk
 "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms
diff --git a/doc/src/compute_bond_local.txt b/doc/src/compute_bond_local.txt
index 6055d28770..889741753a 100644
--- a/doc/src/compute_bond_local.txt
+++ b/doc/src/compute_bond_local.txt
@@ -15,10 +15,11 @@ compute ID group-ID bond/local value1 value2 ... keyword args ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 bond/local = style name of this compute command :l
 one or more values may be appended :l
-value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l
+value = {dist} or {engpot} or {force} or {fx} or {fy} or {fz} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l
   {dist} = bond distance
   {engpot} = bond potential energy
   {force} = bond force :pre
+  {fx},{fy},{fz} = components of bond force
   {engvib} = bond kinetic energy of vibration
   {engrot} = bond kinetic energy of rotation
   {engtrans} = bond kinetic energy of translation
@@ -38,6 +39,7 @@ keyword = {set} :l
 
 compute 1 all bond/local engpot
 compute 1 all bond/local dist engpot force :pre
+compute 1 all bond/local dist fx fy fz :pre
 compute 1 all angle/local dist v_distsq set dist d :pre
 
 [Description:]
@@ -59,6 +61,9 @@ based on the current separation of the pair of atoms in the bond.
 The value {force} is the magnitude of the force acting between the
 pair of atoms in the bond.
 
+The values {fx}, {fy}, and {fz} are the xyz components of
+{force} between the pair of atoms in the bond.
+
 The remaining properties are all computed for motion of the two atoms
 relative to the center of mass (COM) velocity of the 2 atoms in the
 bond.
diff --git a/doc/src/compute_chunk_spread_atom.txt b/doc/src/compute_chunk_spread_atom.txt
index 4afb62683e..c84fe679ee 100644
--- a/doc/src/compute_chunk_spread_atom.txt
+++ b/doc/src/compute_chunk_spread_atom.txt
@@ -30,11 +30,18 @@ compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration :pre
 [Description:]
 
 Define a calculation that "spreads" one or more per-chunk values to
-each atom in the chunk.  This can be useful for creating a "dump
-file"_dump.html where each atom lists info about the chunk it is in,
-e.g. for post-processing purposes.  It can also be used in "atom-style
-variables"_variable.html that need info about the chunk each atom is
-in.  Examples are given below.
+each atom in the chunk.  This can be useful in several scenarios:
+
+For creating a "dump file"_dump.html where each atom lists info about
+the chunk it is in, e.g. for post-processing purposes. :ulb,l
+
+To access chunk value in "atom-style variables"_variable.html that
+need info about the chunk each atom is in. :l
+
+To use the "fix ave/chunk"_fix_ave_chunk.html command to spatially
+average per-chunk values calculated by a per-chunk compute. :l,ule
+
+Examples are given below.
 
 In LAMMPS, chunks are collections of atoms defined by a "compute
 chunk/atom"_compute_chunk_atom.html command, which assigns each atom
@@ -148,6 +155,28 @@ thermo_style    custom step etotal press v_ave :pre
 
 :line
 
+Here is an example for using one set of chunks, defined for molecules,
+to compute the dipole moment vector for each chunk.  E.g. for water
+molecules. Then spreading those values to each atom in each chunk.
+Then defining a second set of chunks based on spatial bins.  And
+finally, using the "fix ave/chunk"_fix_ave_chunk.html command to
+calculate an average dipole moment vector per spatial bin.
+
+compute       cmol all chunk/atom molecule
+compute       dipole all dipole/chunk cmol
+compute       spread all chunk/spread/atom cmol c_dipole\[1\] c_dipole\[2\] c_dipole\[3\]
+compute       cspatial all chunk/atom bin/1d z lower 0.1 units reduced
+fix           ave all ave/chunk 100 10 1000 cspatial c_spread\[*\] :pre
+
+Note that the "fix ave/chunk"_fix_ave_chunk.html command requires
+per-atom values as input.  That is why the compute chunk/spread/atom
+command is used to assign per-chunk values to each atom in the chunk.
+If a molecule straddles bin boundaries, each of its atoms contributes
+in a weighted manner to the average dipole moment of the spatial bin
+it is in.
+
+:line
+
 [Output info:]
 
 This compute calculates a per-atom vector or array, which can be
diff --git a/doc/src/compute_gyration.txt b/doc/src/compute_gyration.txt
index 8deeddf585..054ac02007 100644
--- a/doc/src/compute_gyration.txt
+++ b/doc/src/compute_gyration.txt
@@ -67,6 +67,7 @@ distance^2 "units"_units.html respectively.
 
 [Related commands:]
 
-"compute gyration/chunk"_compute_gyration_chunk.html
+"compute gyration/chunk"_compute_gyration_chunk.html,
+"compute gyration/shape"_compute_gyration_shape.html
 
 [Default:] none
diff --git a/doc/src/compute_gyration_shape.txt b/doc/src/compute_gyration_shape.txt
new file mode 100644
index 0000000000..7c428aea8a
--- /dev/null
+++ b/doc/src/compute_gyration_shape.txt
@@ -0,0 +1,86 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+compute gyration/shape command :h3
+
+[Syntax:]
+
+compute ID group-ID gyration compute-ID :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+gyration/shape = style name of this compute command
+compute-ID = ID of "compute gyration"_compute_gyration.html command :ul
+
+[Examples:]
+
+compute 1 molecule gyration/shape pe :pre
+
+[Description:]
+
+Define a computation that calculates the eigenvalues of the gyration tensor of a
+group of atoms and three shape parameters. The computation includes all effects
+due to atoms passing thru periodic boundaries.
+
+The three computed shape parameters are the asphericity, b, the acylindricity, c,
+and the relative shape anisotropy, k:
+
+:c,image(Eqs/compute_shape_parameters.jpg)
+
+where lx <= ly <= lz are the three eigenvalues of the gyration tensor.
+The asphericity  is always non-negative and zero only when the three principal
+moments are equal. This zero condition is met when the distribution of particles
+is spherically symmetric (hence the name asphericity) but also whenever the particle
+distribution is symmetric with respect to the three coordinate axes, e.g.,
+when the particles are distributed uniformly on a cube, tetrahedron or other Platonic
+solid. The acylindricity is always non-negative and zero only when the two principal
+moments are equal. This zero condition is met when the distribution of particles is
+cylindrically symmetric (hence the name, acylindricity), but also whenever the particle
+distribution is symmetric with respect to the two coordinate axes, e.g., when the
+particles are distributed uniformly on a regular prism. the relative shape anisotropy
+is bounded between zero (if all points are spherically symmetric) and one
+(if all points lie on a line).
+
+NOTE: The coordinates of an atom contribute to the gyration tensor in
+"unwrapped" form, by using the image flags associated with each atom.
+See the "dump custom"_dump.html command for a discussion of "unwrapped"
+coordinates. See the Atoms section of the "read_data"_read_data.html
+command for a discussion of image flags and how they are set for each
+atom.  You can reset the image flags (e.g. to 0) before invoking this
+compute by using the "set image"_set.html command.
+
+[Output info:]
+
+This compute calculates a global vector of
+length 6, which can be accessed by indices 1-6. The first three values are the
+eigenvalues of the gyration tensor followed by the asphericity, the acylindricity
+and the relative shape anisotropy.  The computed values can be used by any command
+that uses global  vector values from a compute as input.  See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
+options.
+
+The vector values calculated by this compute are
+"intensive".  The first five vector values will be in
+distance^2 "units"_units.html while the sixth one is dimensionless.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"compute gyration"_compute_gyration.html
+
+[Default:] none
+
+:line
+
+:link(Theodorou)
+[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).
+
diff --git a/doc/src/compute_hexorder_atom.txt b/doc/src/compute_hexorder_atom.txt
index 082a3cad7a..3c58c3f4dd 100644
--- a/doc/src/compute_hexorder_atom.txt
+++ b/doc/src/compute_hexorder_atom.txt
@@ -65,7 +65,7 @@ In an isotropic liquid, local neighborhoods may still exhibit
 weak hexagonal symmetry, but because the orientational correlation
 decays quickly with distance, the value of phi will be different for
 different atoms, and so when {q}6 is averaged over all the atoms
-in the system, \|<{q}6>\| << 1.
+in the system, |<{q}6>| << 1.
 
 The value of {qn} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
diff --git a/doc/src/compute_hma.txt b/doc/src/compute_hma.txt
new file mode 100644
index 0000000000..4ab355abd7
--- /dev/null
+++ b/doc/src/compute_hma.txt
@@ -0,0 +1,184 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute hma command :h3
+
+[Syntax:]
+
+compute ID group-ID hma temp-ID keyword ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command :l
+hma = style name of this compute command :l
+temp-ID = ID of fix that specifies the set temperature during canonical simulation :l
+keyword = {anharmonic} {u} {p Pharm} {cv} :l
+  {anharmonic} = compute will return anharmonic property values
+  {u} = compute will return potential energy
+  {p} = compute will return pressure.  the following keyword must be the difference between the harmonic pressure and lattice pressure as described below
+  {cv} = compute will return the heat capacity :pre
+:ule
+
+[Examples:]
+
+compute 2 all hma 1 u
+compute 2 all hma 1 anharmonic u p 0.9
+compute 2 all hma 1 u cv :pre
+
+
+
+[Description:]
+
+Define a computation that calculates the properties of a solid (potential
+energy, pressure or heat capacity), using the harmonically-mapped averaging
+(HMA) method. 
+This command yields much higher precision than the equivalent compute commands
+("compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html, etc.)
+commands during a canonical simulation of an atomic crystal. Specifically,
+near melting HMA can yield averages of a given precision an order of magnitude
+faster than conventional methods, and this only improves as the temperatures is
+lowered.  This is particularly important for evaluating the free energy by
+thermodynamic integration, where the low-temperature contributions are the
+greatest source of statistical uncertainty.  Moreover, HMA has other
+advantages, including smaller potential-truncation effects, finite-size
+effects, smaller timestep inaccuracy, faster equilibration and shorter
+decorrelation time.
+
+HMA should not be used if atoms are expected to diffuse.  It is also
+restricted to simulations in the NVT ensemble.  While this compute may be
+used with any potential in LAMMPS, it will provide inaccurate results
+for potentials that do not go to 0 at the truncation distance;
+"pair_lj_smooth_linear"_pair_lj_smooth_linear.html and Ewald summation should
+work fine, while "pair_lj"_pair_lj.html will perform poorly unless 
+the potential is shifted (via "pair_modify"_pair_modify.html shift) or the cutoff is large.  Furthermore, computation of the heat capacity with
+this compute is restricted to those that implement the single_hessian method
+in Pair.  Implementing single_hessian in additional pair styles is simple.
+Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at
+buffalo.edu) if your desired pair style does not have this method.  This is
+the list of pair styles that currently implement pair_hessian:
+
+"lj_smooth_linear"_pair_lj_smooth_linear.html :l
+:ule
+
+In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble
+averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination 
+by noise produced by the already-known harmonic behavior. 
+A detailed description of this method can be found in ("Moustafa"_#hma-Moustafa). The potential energy is computed by the formula:
+
+\begin\{equation\}
+\left< U\right>_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B T  + \left< U + \frac\{1\}\{2\} F\bullet\Delta r \right>
+\end\{equation\}
+
+where \(N\) is the number of atoms in the system, \(k_B\) is Boltzmann's
+constant, \(T\) is the temperature, \(d\) is the
+dimensionality of the system (2 or 3 for 2d/3d), \(F\bullet\Delta r\) is the sum of dot products of the 
+atomic force vectors and displacement (from lattice sites) vectors, and \(U\) is the sum of 
+pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies. 
+
+The pressure is computed by the formula:
+
+\begin\{equation\}
+\left< P\right>_\{HMA\} = \Delta \hat P + \left< P_\{vir\} + \frac\{\beta \Delta \hat P - \rho\}\{d(N-1)\} F\bullet\Delta r \right>
+\end\{equation\}
+
+where \(\rho\) is the number density of the system, \(\Delta \hat P\) is the
+difference between the harmonic and lattice pressure, \(P_\{vir\}\) is
+the virial pressure computed as the sum of pair, bond, angle, dihedral,
+improper, kspace (long-range), and fix contributions to the force on each
+atom, and \(k_B=1/k_B T\).  Although the method will work for any value of \(\Delta \hat P\)
+specified (use pressure "units"_units.html), the precision of the resultant
+pressure is sensitive to \(\Delta \hat P\); the precision tends to be
+best when \(\Delta \hat P\) is the actual the difference between the lattice
+pressure and harmonic pressure.
+
+\begin\{equation\}
+\left<C_V \right>_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B + \frac\{1\}\{k_B T^2\} \left( \left<
+U_\{HMA\}^2 \right> - \left<U_\{HMA\}\right>^2 \right) + \frac\{1\}\{4 T\}
+\left< F\bullet\Delta r + \Delta r \bullet \Phi \bullet \Delta r \right>
+\end\{equation\}
+
+where \(\Phi\) is the Hessian matrix. The compute hma command
+computes the full expression for \(C_V\) except for the
+\(\left<U_\{HMA\}^2\right>^2\) in the variance term, which can be obtained by
+passing the {u} keyword; you must add this extra contribution to the \(C_V\)
+value reported by this compute.  The variance term can cause significant
+round-off error when computing \(C_V\).  To address this, the {anharmonic}
+keyword can be passed and/or the output format can be specified with more
+digits.
+
+thermo_modify format float '%22.15e' :pre
+
+The {anharmonic} keyword will instruct the compute to return anharmonic
+properties rather than the full properties, which include lattice, harmonic
+and anharmonic contributions.
+When using this keyword, the compute must be first active (it must be included
+via a "thermo_style custom"_thermo_style.html command) while the atoms are
+still at their lattice sites (before equilibration).
+
+The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover ("fix nvt"_fix_nh.html) or 
+Berendsen ("fix temp/berendsen"_fix_temp_berendsen.html) thermostat used for the simulation. While using this command, Langevin thermostat 
+("fix langevin"_fix_langevin.html) 
+should be avoided as its extra forces interfere with the HMA implementation. 
+
+ 
+
+NOTE: Compute hma command should be used right after the energy minimization, when the atoms are at their lattice sites. 
+The simulation should not be started before this command has been used in the input script.
+
+
+The following example illustrates the placement of this command in the input script:
+
+
+min_style cg 
+minimize 1e-35 1e-15 50000 500000 
+compute 1 all hma thermostatid u
+fix thermostatid all nvt temp 600.0 600.0 100.0 :pre  
+
+
+
+NOTE: Compute hma should be used when the atoms of the solid do not diffuse. Diffusion will reduce the precision in the potential energy computation.
+
+ 
+NOTE: The "fix_modify energy yes"_fix_modify.html command must also be specified if a fix is to contribute potential energy to this command.
+
+An example input script that uses this compute is included in
+examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA
+properties fluctuate less than the corresponding conventional properties.
+
+[Output info:]
+
+This compute calculates a global vector that includes the n properties
+requested as arguments to the command (the potential energy, pressure and/or heat
+capacity).  The elements of the vector can be accessed by indices 1-n by any
+command that uses global vector values as input.  See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output options.
+
+The vector values calculated by this compute are "extensive".  The
+scalar value will be in energy "units"_units.html.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is enabled only
+if LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+Usage restricted to canonical (NVT) ensemble simulation only.
+
+[Related commands:]
+
+"compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html
+
+"dynamical matrix"_dynamical_matrix.html provides a finite difference
+formulation of the hessian provided by Pair's single_hessian, which is used by
+this compute.
+
+[Default:] none
+
+:line
+
+:link(hma-Moustafa)
+[(Moustafa)] Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, {Very fast averaging of thermal properties of crystals by molecular simulation}, 
+"Phys. Rev. E \[92\], 043303 (2015)"_https://link.aps.org/doi/10.1103/PhysRevE.92.043303
diff --git a/doc/src/compute_momentum.txt b/doc/src/compute_momentum.txt
new file mode 100644
index 0000000000..2c6ec78cf3
--- /dev/null
+++ b/doc/src/compute_momentum.txt
@@ -0,0 +1,49 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+compute momentum command :h3
+
+[Syntax:]
+
+compute ID group-ID momentum :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+momentum = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all momentum :pre
+
+[Description:]
+
+Define a computation that calculates the translational momentum
+of a group of particles.
+
+The momentum of each particles is computed as m v, where m and v are
+the mass and velocity of the particle.
+
+[Output info:]
+
+This compute calculates a global vector (the summed momentum) of
+length 3. This value can be used by any command that uses a global
+vector value from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
+options.
+
+The vector value calculated by this compute is "extensive". The vector
+value will be in mass*velocity "units"_units.html.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+[Default:] none
diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt
index 7327a7b1d3..da14c866bd 100644
--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@@ -19,6 +19,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
   {cutoff} value = distance cutoff
   {nnn} value = number of nearest neighbors
   {degrees} values = nlvalues, l1, l2,...
+  {wl} value = yes or no
+  {wl/hat} value = yes or no
   {components} value = ldegree  :pre
 
 :ule
@@ -27,7 +29,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
 
 compute 1 all orientorder/atom
 compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
-compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre
+compute 1 all orientorder/atom wl/hat yes
+compute 1 all orientorder/atom components 6 :pre
 
 [Description:]
 
@@ -48,7 +51,7 @@ neighbors of the central atom.
 The angles theta and phi are the standard spherical polar angles
 defining the direction of the bond vector {rij}.
 The second equation defines {Ql}, which is a
-rotationally invariant scalar quantity obtained by summing
+rotationally invariant non-negative amplitude obtained by summing
 over all the components of degree {l}.
 
 The optional keyword {cutoff} defines the distance cutoff
@@ -63,7 +66,7 @@ specified distance cutoff are used.
 
 The optional keyword {degrees} defines the list of order parameters to
 be computed.  The first argument {nlvalues} is the number of order
-parameters. This is followed by that number of integers giving the
+parameters. This is followed by that number of non-negative integers giving the
 degree of each order parameter. Because {Q}2 and all odd-degree order
 parameters are zero for atoms in cubic crystals (see
 "Steinhardt"_#Steinhardt), the default order parameters are {Q}4,
@@ -71,7 +74,20 @@ parameters are zero for atoms in cubic crystals (see
 = sqrt(7/3)/8 = 0.19094....  The numerical values of all order
 parameters up to {Q}12 for a range of commonly encountered
 high-symmetry structures are given in Table I of "Mickel et
-al."_#Mickel.
+al."_#Mickel, and these can be reproduced with this compute
+
+The optional keyword {wl} will output the third-order invariants {Wl} 
+(see Eq. 1.4 in "Steinhardt"_#Steinhardt) for the same degrees as
+for the {Ql} parameters. For the FCC crystal with {nnn} =12,
+{W}4 = -sqrt(14/143).(49/4096)/Pi^1.5 = -0.0006722136...
+
+The optional keyword {wl/hat} will output the normalized third-order 
+invariants {Wlhat} (see Eq. 2.2 in "Steinhardt"_#Steinhardt) 
+for the same degrees as for the {Ql} parameters. For the FCC crystal 
+with {nnn} =12, {W}4hat = -7/3*sqrt(2/429) = -0.159317...The numerical
+values of {Wlhat} for a range of commonly encountered high-symmetry
+structures are given in Table I of "Steinhardt"_#Steinhardt, and these
+can be reproduced with this keyword.
 
 The optional keyword {components} will output the components of the
 normalized complex vector {Ybar_lm} of degree {ldegree}, which must be
@@ -82,7 +98,7 @@ particles, as discussed in "ten Wolde"_#tenWolde2.
 
 The value of {Ql} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
-{nnn} neighbors within the distance cutoff.
+{nnn} neighbors within the distance cutoff, unless {nnn} is NULL.
 
 The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
@@ -108,6 +124,12 @@ This compute calculates a per-atom array with {nlvalues} columns,
 giving the {Ql} values for each atom, which are real numbers on the
 range 0 <= {Ql} <= 1.
 
+If the keyword {wl} is set to yes, then the {Wl} values for each
+atom will be added to the output array, which are real numbers.
+
+If the keyword {wl/hat} is set to yes, then the {Wl_hat} 
+values for each atom will be added to the output array, which are real numbers.
+ 
 If the keyword {components} is set, then the real and imaginary parts
 of each component of (normalized) {Ybar_lm} will be added to the
 output array in the following order: Re({Ybar_-m}) Im({Ybar_-m})
@@ -130,7 +152,8 @@ hexorder/atom"_compute_hexorder_atom.html
 [Default:]
 
 The option defaults are {cutoff} = pair style cutoff, {nnn} = 12,
-{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
+{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12,
+{wl} = no, {wl/hat} = no, and {components} off
 
 :line
 
diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt
index bd6e38e392..9b27413cfc 100644
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@@ -16,12 +16,13 @@ ID, group-ID are documented in "compute"_compute.html command
 pressure = style name of this compute command
 temp-ID = ID of compute that calculates temperature, can be NULL if not needed
 zero or more keywords may be appended
-keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul
+keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} or {pair/hybrid} :ul
 
 [Examples:]
 
 compute 1 all pressure thermo_temp
-compute 1 all pressure NULL pair bond :pre
+compute 1 all pressure NULL pair bond
+compute 1 all pressure NULL pair/hybrid lj/cut :pre
 
 [Description:]
 
@@ -67,6 +68,9 @@ extra keywords are listed, then only those components are summed to
 compute temperature or ke and/or the virial.  The {virial} keyword
 means include all terms except the kinetic energy {ke}.
 
+The {pair/hybrid} keyword means to only include contribution
+from a sub-style in a {hybrid} or {hybrid/overlay} pair style.
+
 Details of how LAMMPS computes the virial efficiently for the entire
 system, including for many-body potentials and accounting for the
 effects of periodic boundary conditions are discussed in
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
index 926b8da222..b24387e856 100644
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@@ -44,8 +44,10 @@ Computes :h1
    compute_group_group
    compute_gyration
    compute_gyration_chunk
+   compute_gyration_shape
    compute_heat_flux
    compute_hexorder_atom
+   compute_hma
    compute_improper
    compute_improper_local
    compute_inertia_chunk
@@ -57,6 +59,7 @@ Computes :h1
    compute_meso_e_atom
    compute_meso_rho_atom
    compute_meso_t_atom
+   compute_momentum
    compute_msd
    compute_msd_chunk
    compute_msd_nongauss
diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt
index d80e2d45f1..2c97194cba 100644
--- a/doc/src/create_atoms.txt
+++ b/doc/src/create_atoms.txt
@@ -242,9 +242,8 @@ write_dump      all atom sinusoid.lammpstrj :pre
 
 :c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
 
-The {rotate} keyword can only be used with the {single} style and
-when adding a single molecule. It allows to specify the orientation
-at which the molecule is inserted.  The axis of rotation is
+The {rotate} keyword allows specification of the orientation
+at which molecules are inserted.  The axis of rotation is
 determined by the rotation vector (Rx,Ry,Rz) that goes through the
 insertion point.  The specified {theta} determines the angle of
 rotation around that axis.  Note that the direction of rotation for
diff --git a/doc/src/dynamical_matrix.txt b/doc/src/dynamical_matrix.txt
index a7dc4e442e..6291bdec52 100644
--- a/doc/src/dynamical_matrix.txt
+++ b/doc/src/dynamical_matrix.txt
@@ -47,6 +47,9 @@ package"_Build_package.html doc page for more info.
 
 "fix phonon"_fix_phonon.html
 
+"compute hma"_compute_hma.html uses an analytic formulation of the hessian
+provided by Pair's single_hessian.
+
 [Default:]
 
 The default settings are file = "dynmat.dyn", binary = no  
diff --git a/doc/src/fix.txt b/doc/src/fix.txt
index 294802c4fa..1dd9cc9f1b 100644
--- a/doc/src/fix.txt
+++ b/doc/src/fix.txt
@@ -165,40 +165,40 @@ page are followed by one or more of (g,i,k,o,t) to indicate which
 accelerated styles exist.
 
 "adapt"_fix_adapt.html - change a simulation parameter over time
-"adapt/fep"_fix_adapt_fep.html -
+"adapt/fep"_fix_adapt_fep.html - enhanced version of fix adapt
 "addforce"_fix_addforce.html - add a force to each atom
-"addtorque"_fix_addtorque.html -
+"addtorque"_fix_addtorque.html - add a torque to a group of atoms
 "append/atoms"_fix_append_atoms.html - append atoms to a running simulation
-"atc"_fix_atc.html -
+"atc"_fix_atc.html - initiates a coupled MD/FE simulation
 "atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping
 "ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
 "ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities
 "ave/correlate"_fix_ave_correlate.html - compute/output time correlations
 "ave/correlate/long"_fix_ave_correlate_long.html -
 "ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms
-"ave/histo/weight"_fix_ave_histo.html -
+"ave/histo/weight"_fix_ave_histo.html - weighted version of fix ave/histo
 "ave/time"_fix_ave_time.html - compute/output global time-averaged quantities
 "aveforce"_fix_aveforce.html - add an averaged force to each atom
 "balance"_fix_balance.html - perform dynamic load-balancing
-"bocs"_fix_bocs.html -
+"bocs"_fix_bocs.html - NPT style time integration with pressure correction
 "bond/break"_fix_bond_break.html - break bonds on the fly
 "bond/create"_fix_bond_create.html - create bonds on the fly
-"bond/react"_fix_bond_react.html -
+"bond/react"_fix_bond_react.html - apply topology changes to model reactions
 "bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
 "box/relax"_fix_box_relax.html - relax box size during energy minimization
-"client/md"_fix_client_md.html -
-"cmap"_fix_cmap.html -
-"colvars"_fix_colvars.html -
-"controller"_fix_controller.html -
+"client/md"_fix_client_md.html - MD client for client/server simulations
+"cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field
+"colvars"_fix_colvars.html - interface to the collective variables “Colvars” library
+"controller"_fix_controller.html - apply control loop feedback mechanism
 "deform"_fix_deform.html - change the simulation box size/shape
 "deposit"_fix_deposit.html - add new atoms above a surface
-"dpd/energy"_fix_dpd_energy.html -
+"dpd/energy"_fix_dpd_energy.html - constant energy dissipative particle dynamics
 "drag"_fix_drag.html - drag atoms towards a defined coordinate
-"drude"_fix_drude.html -
-"drude/transform/direct"_fix_drude_transform.html -
-"drude/transform/inverse"_fix_drude_transform.html -
+"drude"_fix_drude.html - part of Drude oscillator polarization model
+"drude/transform/direct"_fix_drude_transform.html -  part of Drude oscillator polarization model
+"drude/transform/inverse"_fix_drude_transform.html -  part of Drude oscillator polarization model
 "dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
-"edpd/source"_fix_dpd_source.html -
+"edpd/source"_fix_dpd_source.html - add heat source to eDPD simulations
 "efield"_fix_efield.html - impose electric field on system
 "ehex"_fix_ehex.html - enhanced heat exchange algorithm
 "electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force
@@ -208,27 +208,26 @@ accelerated styles exist.
 "eos/table/rx"_fix_eos_table_rx.html -
 "evaporate"_fix_evaporate.html - remove atoms from simulation periodically
 "external"_fix_external.html - callback to an external driver program
-"ffl"_fix_ffl.html -
-"filter/corotate"_fix_filter_corotate.html -
-"flow/gauss"_fix_flow_gauss.html -
+"ffl"_fix_ffl.html - apply a Fast-Forward Langevin equation thermostat
+"filter/corotate"_fix_filter_corotate.html - implement corotation filter to allow larger timesteps with r-RESPA
+"flow/gauss"_fix_flow_gauss.html - Gaussian dynamics for constant mass flux
 "freeze"_fix_freeze.html - freeze atoms in a granular simulation
 "gcmc"_fix_gcmc.html - grand canonical insertions/deletions
-"gld"_fix_gcmc.html - generalized Langevin dynamics integrator
-"gld"_fix_gld.html -
-"gle"_fix_gle.html -
+"gld"_fix_gld.html - generalized Langevin dynamics integrator
+"gle"_fix_gle.html - generalized Langevin equation thermostat
 "gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
-"grem"_fix_grem.html -
+"grem"_fix_grem.html - implements the generalized replica exchange method
 "halt"_fix_halt.html - terminate a dynamics run or minimization
 "heat"_fix_heat.html - add/subtract momentum-conserving heat
 "hyper/global"_fix_hyper_global.html - global hyperdynamics
 "hyper/local"_fix_hyper_local.html - local hyperdynamics
-"imd"_fix_imd.html -
+"imd"_fix_imd.html - implements the “Interactive MD” (IMD) protocol 
 "indent"_fix_indent.html - impose force due to an indenter
-"ipi"_fix_ipi.html -
+"ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations
 "langevin"_fix_langevin.html - Langevin temperature control
-"langevin/drude"_fix_langevin_drude.html -
-"langevin/eff"_fix_langevin_eff.html -
-"langevin/spin"_fix_langevin_spin.html -
+"langevin/drude"_fix_langevin_drude.html - Langevin temperature control of Drude oscillators
+"langevin/eff"_fix_langevin_eff.html - Langevin temperature control for the electron force field model
+"langevin/spin"_fix_langevin_spin.html - Langevin temperature control for a spin or spin-lattice system
 "latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
 "lb/fluid"_fix_lb_fluid.html -
 "lb/momentum"_fix_lb_momentum.html -
@@ -236,64 +235,60 @@ accelerated styles exist.
 "lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html -
 "lb/viscous"_fix_lb_viscous.html -
 "lineforce"_fix_lineforce.html - constrain atoms to move in a line
-"manifoldforce"_fix_manifoldforce.html -
-"meso"_fix_meso.html -
-"meso"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
-"meso/move"_fix_meso_move.html -
+"manifoldforce"_fix_manifoldforce.html - restrain atoms to a manifold during minimization
+"meso"_fix_meso.html - time integration for SPH/DPDE particles
+"meso/move"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
 "meso/stationary"_fix_meso_stationary.html -
 "momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms
 "move"_fix_move.html - move atoms in a prescribed fashion
-"mscg"_fix_mscg.html -
+"mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models
 "msst"_fix_msst.html - multi-scale shock technique (MSST) integration
-"mvv/dpd"_fix_mvv_dpd.html -
-"mvv/edpd"_fix_mvv_dpd.html -
-"mvv/tdpd"_fix_mvv_dpd.html -
+"mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm
+"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algorithm
+"mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm
 "neb"_fix_neb.html - nudged elastic band (NEB) spring forces
 "nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
 "nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
-"nph/body"_fix_nph_body.html -
-"nph/body"_fix_nve_body.html - NPH for body particles
-"nph/eff"_fix_nh_eff.html -
+"nph/body"_fix_nph_body.html - NPH for body particles
+"nph/eff"_fix_nh_eff.html - NPH for  nuclei and electrons in the electron force field model
 "nph/sphere"_fix_nph_sphere.html - NPH for spherical particles
 "nphug"_fix_nphug.html - constant-stress Hugoniostat integration
 "npt"_fix_nh.html - constant NPT time integration via Nose/Hoover
 "npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
-"npt/body"_fix_npt_body.html -
-"npt/body"_fix_nve_body.html - NPT for body particles
-"npt/eff"_fix_nh_eff.html -
+"npt/body"_fix_npt_body.html - NPT for body particles
+"npt/eff"_fix_nh_eff.html - NPT for  nuclei and electrons in the electron force field model
 "npt/sphere"_fix_npt_sphere.html - NPT for spherical particles
-"npt/uef"_fix_nh_uef.html -
+"npt/uef"_fix_nh_uef.html - NPT style time integration with diagonal flow
 "nve"_fix_nve.html - constant NVE time integration
 "nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles
-"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces"
-"nve/awpmd"_fix_nve_awpmd.html -
+"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces
+"nve/awpmd"_fix_nve_awpmd.html - NVE for the Antisymmetrized Wave Packet Molecular Dynamics model
 "nve/body"_fix_nve_body.html - NVE for body particles
-"nve/dot"_fix_nve_dot.html -
-"nve/dotc/langevin"_fix_nve_dotc_langevin.html -
-"nve/eff"_fix_nve_eff.html -
+"nve/dot"_fix_nve_dot.html - rigid body constant energy time integrator for coarse grain models
+"nve/dotc/langevin"_fix_nve_dotc_langevin.html - Langevin style rigid body time integrator for coarse grain models
+"nve/eff"_fix_nve_eff.html - NVE for  nuclei and electrons in the electron force field model
 "nve/limit"_fix_nve_limit.html - NVE with limited step length
 "nve/line"_fix_nve_line.html - NVE for line segments
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html -
 "nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
 "nve/sphere"_fix_nve_sphere.html - NVE for spherical particles
-"nve/spin"_fix_nve_spin.html -
+"nve/spin"_fix_nve_spin.html - NVE for a spin or spin-lattice system
 "nve/tri"_fix_nve_tri.html - NVE for triangles
-"nvk"_fix_nvk.html -
-"nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover
+"nvk"_fix_nvk.html - constant kinetic energy time integration
+"nvt"_fix_nh.html - NVT time integration via Nose/Hoover
 "nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
-"nvt/body"_fix_nve_body.html - NVT for body particles
-"nvt/body"_fix_nvt_body.html -
-"nvt/eff"_fix_nh_eff.html -
+"nvt/body"_fix_nvt_body.html - NVT for body particles
+"nvt/eff"_fix_nh_eff.html - NVE for  nuclei and electrons in the electron force field model
 "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html -
 "nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
-"nvt/sllod/eff"_fix_nvt_sllod_eff.html -
+"nvt/sllod/eff"_fix_nvt_sllod_eff.html - NVT for NEMD with SLLOD equations for the electron force field model
 "nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
-"nvt/uef"_fix_nh_uef.html -
+"nvt/uef"_fix_nh_uef.html - NVT style time integration with diagonal flow
 "oneway"_fix_oneway.html - constrain particles on move in one direction
 "orient/bcc"_fix_orient.html - add grain boundary migration force for BCC
 "orient/fcc"_fix_orient.html - add grain boundary migration force for FCC
-"phonon"_fix_phonon.html -
-"pimd"_fix_pimd.html -
+"phonon"_fix_phonon.html - calculate dynamical matrix from MD simulations
+"pimd"_fix_pimd.html - Feynman path integral molecular dynamics
 "planeforce"_fix_planeforce.html - constrain atoms to move in a plane
 "plumed"_fix_plumed.html - wrapper on PLUMED free energy library
 "poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies
@@ -302,24 +297,24 @@ accelerated styles exist.
 "press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat
 "print"_fix_print.html - print text and variables during a simulation
 "property/atom"_fix_property_atom.html - add customized per-atom values
-"python/invoke"_fix_python_invoke.html -
-"python/move"_fix_python_move.html -
-"qbmsst"_fix_qbmsst.html -
+"python/invoke"_fix_python_invoke.html - call a Python function during a simulation
+"python/move"_fix_python_move.html -  call a Python function during a simulation run
+"qbmsst"_fix_qbmsst.html - quantum bath multi-scale shock technique time integrator
 "qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential
 "qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method
 "qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer
 "qeq/point"_fix_qeq.html - charge equilibration via point method
-"qeq/reax"_fix_qeq_reax.html -
+"qeq/reax"_fix_qeq_reax.html - charge equilibration for ReaxFF potential
 "qeq/shielded"_fix_qeq.html - charge equilibration via shielded method
 "qeq/slater"_fix_qeq.html - charge equilibration via Slater method
-"qmmm"_fix_qmmm.html -
-"qtb"_fix_qtb.html -
+"qmmm"_fix_qmmm.html - functionality to enable a quantum mechanics/molecular mechanics coupling
+"qtb"_fix_qtb.html - implement quantum thermal bath scheme
 "rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
 "reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
 "reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
 "recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
 "restrain"_fix_restrain.html - constrain a bond, angle, dihedral
-"rhok"_fix_rhok.html -
+"rhok"_fix_rhok.html - add bias potential for long-range ordered systems
 "rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration
 "rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
 "rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration
@@ -332,11 +327,11 @@ accelerated styles exist.
 "rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
 "rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
 "rx"_fix_rx.html -
-"saed/vtk"_fix_saed_vtk.html -
+"saed/vtk"_fix_saed_vtk.html - 
 "setforce"_fix_setforce.html - set the force on each atom
 "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
-"shardlow"_fix_shardlow.html -
-"smd"_fix_smd.html -
+"shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting
+"smd"_fix_smd.html - applied a steered MD force to a group
 "smd/adjust_dt"_fix_smd_adjust_dt.html -
 "smd/integrate_tlsph"_fix_smd_integrate_tlsph.html -
 "smd/integrate_ulsph"_fix_smd_integrate_ulsph.html -
@@ -355,13 +350,13 @@ accelerated styles exist.
 "temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics
 "temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics
 "temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling
-"temp/rescale/eff"_fix_temp_rescale_eff.html -
+"temp/rescale/eff"_fix_temp_rescale_eff.html - temperature control by velocity rescaling in the electron force field model
 "tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method
 "thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
 "ti/spring"_fix_ti_spring.html -
 "tmd"_fix_tmd.html - guide a group of atoms to a new configuration
 "ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling
-"ttm/mod"_fix_ttm.html -
+"ttm/mod"_fix_ttm.html - enhanced two-temperature model with additional options
 "tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters
 "vector"_fix_vector.html - accumulate a global vector every N timesteps
 "viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation
@@ -369,17 +364,18 @@ accelerated styles exist.
 "wall/body/polygon"_fix_wall_body_polygon.html -
 "wall/body/polyhedron"_fix_wall_body_polyhedron.html -
 "wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles
-"wall/ees"_fix_wall_ees.html -
+"wall/ees"_fix_wall_ees.html - wall for ellipsoidal particles
 "wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations
 "wall/gran/region"_fix_wall_gran_region.html -
 "wall/harmonic"_fix_wall.html - harmonic spring wall
 "wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall
 "wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall
 "wall/lj93"_fix_wall.html - Lennard-Jones 9-3 wall
+"wall/morse"_fix_wall.html - Morse potential wall
 "wall/piston"_fix_wall_piston.html - moving reflective piston wall
 "wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
 "wall/region"_fix_wall_region.html - use region surface as wall
-"wall/region/ees"_fix_wall_ees.html -
+"wall/region/ees"_fix_wall_ees.html - use region surface as wall for ellipsoidal particles
 "wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul
 
 [Restrictions:]
diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt
index 0d862a890d..4f047ec42d 100644
--- a/doc/src/fix_adapt.txt
+++ b/doc/src/fix_adapt.txt
@@ -149,8 +149,7 @@ meaning of these parameters:
 "spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global:
 "table"_pair_table.html: table_cutoff: type pairs:
 "ufm"_pair_ufm.html: epsilon,sigma: type pairs:
-"soft"_pair_soft.html: a: type pairs:
-"kim"_pair_kim.html: PARAM_FREE_*&#58i,j,...: global :tb(c=3,s=:)
+"soft"_pair_soft.html: a: type pairs: :tb(c=3,s=:)
 
 NOTE: It is easy to add new pairwise potentials and their parameters
 to this list.  All it typically takes is adding an extract() method to
diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt
index db9c35069c..bb7ac3713c 100644
--- a/doc/src/fix_bocs.txt
+++ b/doc/src/fix_bocs.txt
@@ -47,13 +47,13 @@ or {cubic_spline}.
 
 With either spline method, the only argument that needs to follow it
 is the name of a file that contains the desired pressure correction
-as a function of volume. The file should be formatted so each line has:
+as a function of volume. The file must be formatted so each line has:
 
 Volume_i, PressureCorrection_i :pre
 
 Note both the COMMA and the SPACE separating the volume's
 value and its corresponding pressure correction. The volumes in the file
-should be uniformly spaced. Both the volumes and the pressure corrections
+must be uniformly spaced. Both the volumes and the pressure corrections
 should be provided in the proper units, e.g. if you are using {units real},
 the volumes should all be in cubic angstroms, and the pressure corrections
 should all be in atmospheres. Furthermore, the table should start/end at a
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index 34f0e6daf7..3f428e2103 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -24,7 +24,7 @@ common_keyword = {stabilization} :l
   {stabilization} values = {no} or {yes} {group-ID} {xmax}
     {no} = no reaction site stabilization
     {yes} = perform reaction site stabilization
-      {group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms
+      {group-ID} = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction
       {xmax} = xmax value that is used by an internally-created "nve/limit"_fix_nve_limit.html integrator :pre
 react = mandatory argument indicating new reaction specification :l
   react-ID = user-assigned name for the reaction :l
@@ -52,6 +52,8 @@ react = mandatory argument indicating new reaction specification :l
 
 [Examples:]
 
+For unabridged example scripts and files, see examples/USER/misc/bond_react.
+
 molecule mol1 pre_reacted_topology.txt
 molecule mol2 post_reacted_topology.txt
 fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
@@ -106,6 +108,20 @@ involved in any new reactions. The {xmax} value keyword should
 typically be set to the maximum distance that non-reacting atoms move
 during the simulation.
 
+Fix bond/react creates and maintains two important dynamic groups of
+atoms when using the {stabilization} keyword. The first group contains
+all atoms currently involved in a reaction; this group is
+automatically thermostatted by an internally-created
+"nve/limit"_fix_nve_limit.html integrator. The second group contains
+all atoms currently not involved in a reaction. This group should be
+used by a thermostat in order to time integrate the system. The name
+of this group of non-reacting atoms is created by appending '_REACT'
+to the group-ID argument of the {stabilization} keyword, as shown in
+the second example above.
+
+NOTE: When using reaction stabilization, you should generally not have
+a separate thermostat which acts on the 'all' group.
+
 The group-ID set using the {stabilization} keyword can be an existing
 static group or a previously-unused group-ID. It cannot be specified
 as 'all'. If the group-ID is previously unused, the fix bond/react
@@ -116,20 +132,17 @@ internally-created dynamic group. In both cases, this new dynamic
 group is named by appending '_REACT' to the group-ID, e.g.
 nvt_grp_REACT. By specifying an existing group, you may thermostat
 constant-topology parts of your system separately. The dynamic group
-contains only non-reacting atoms at a given timestep, and therefore
-should be used by a subsequent system-wide time integrator such as
-nvt, npt, or nve, as shown in the second example above. The time
-integration command should be placed after the fix bond/react command
-due to the internal dynamic grouping performed by fix bond/react.
+contains only atoms not involved in a reaction at a given timestep,
+and therefore should be used by a subsequent system-wide time
+integrator such as nvt, npt, or nve, as shown in the second example
+above (full examples can be found at examples/USER/misc/bond_react).
+The time integration command should be placed after the fix bond/react
+command due to the internal dynamic grouping performed by fix
+bond/react.
 
 NOTE: If the group-ID is an existing static group, react-group-IDs
 should also be specified as this static group, or a subset.
 
-NOTE: If the group-ID is previously unused, the internally-created
-group applies to all atoms in the system, i.e. you should generally
-not have a separate thermostat which acts on the 'all' group, or any
-other group.
-
 The following comments pertain to each {react} argument (in other
 words, can be customized for each reaction, or reaction step):
 
@@ -352,12 +365,13 @@ an atom that is not deleted. In addition to deleting unwanted reaction
 by-products, this feature can be used to remove specific topologies,
 such as small rings, that may be otherwise indistinguishable.
 
-Also, it may be beneficial to ensure reacting atoms are at a certain
-temperature before being released to the overall thermostat. For this,
-you can use the internally-created dynamic group named
-"bond_react_MASTER_group." For example, adding the following command
-would thermostat the group of all atoms currently involved in a
-reaction:
+Optionally, you can enforce additional behaviors on reacting atoms.
+For example, it may be beneficial to force reacting atoms to remain at
+a certain temperature. For this, you can use the internally-created
+dynamic group named "bond_react_MASTER_group", which consists of all
+atoms currently involved in a reaction. For example, adding the
+following command would add an additional thermostat to the group of
+all currently-reacting atoms:
 
 fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre
 
diff --git a/doc/src/fix_plumed.txt b/doc/src/fix_plumed.txt
index 97b3150a0b..86807f531d 100644
--- a/doc/src/fix_plumed.txt
+++ b/doc/src/fix_plumed.txt
@@ -114,5 +114,5 @@ The default options are plumedfile = NULL and outfile = NULL
 :link(PLUMED)
 [(PLUMED)] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
 
-:link(plumeddocs,http://www.plumed.org/documentation)
+:link(plumeddocs,http://www.plumed.org/doc.html)
 :link(plumedhome,http://www.plumed.org/)
diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt
index f013ebfae1..7f0a72d1b3 100644
--- a/doc/src/fix_rhok.txt
+++ b/doc/src/fix_rhok.txt
@@ -39,8 +39,8 @@ An example of using the interface pinning method is located in the
 
 [Restrictions:]
 
-This fix is part of the MISC package.  It is only enabled if LAMMPS
-was built with that package.  See the "Build
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
 package"_Build_package.html doc page for more info.
 
 [Related commands:]
diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt
index 162e32c68c..7868bacf04 100644
--- a/doc/src/fix_wall.txt
+++ b/doc/src/fix_wall.txt
@@ -12,16 +12,18 @@ fix wall/lj126 command :h3
 fix wall/lj1043 command :h3
 fix wall/colloid command :h3
 fix wall/harmonic command :h3
+fix wall/morse command :h3
 
 [Syntax:]
 
 fix ID group-ID style face args ... keyword value ... :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
-style = {wall/lj93} or {wall/lj126} or {wall/lj1043} or {wall/colloid} or {wall/harmonic} :l
+style = {wall/lj93} or {wall/lj126} or {wall/lj1043} or {wall/colloid} or {wall/harmonic} or {wall/morse} :l
 one or more face/arg pairs may be appended :l
 face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
-  args = coord epsilon sigma cutoff
+  args for styles {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} :l
+    args = coord epsilon sigma cutoff
     coord = position of wall = EDGE or constant or variable
       EDGE = current lo or hi edge of simulation box
       constant = number like 0.0 or -30.0 (distance units)
@@ -31,6 +33,19 @@ face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
     sigma = size factor for wall-particle interaction (distance units)
       sigma can be a variable (see below)
     cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
+  args for style {morse} :l
+    args = coord D_0 alpha r_0 cutoff
+    coord = position of wall = EDGE or constant or variable
+      EDGE = current lo or hi edge of simulation box
+      constant = number like 0.0 or -30.0 (distance units)
+      variable = "equal-style variable"_variable.html like v_x or v_wiggle
+    D_0 = depth of the potential (energy units)
+      D_0 can be a variable (see below)
+    alpha = width factor for wall-particle interaction (1/distance units)
+      alpha can be a variable (see below)
+    r_0 = distance of the potential minimum from the face of region (distance units)
+      r_0 can be a variable (see below)
+    cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
 zero or more keyword/value pairs may be appended :l
 keyword = {units} or {fld} :l
   {units} value = {lattice} or {box}
@@ -48,6 +63,7 @@ keyword = {units} or {fld} :l
 
 fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
 fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
+fix wallhi all wall/morse xhi EDGE 1.0 1.0 1.0 2.5 units box
 fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
 fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 :pre
 
@@ -80,6 +96,10 @@ potential:
 
 :c,image(Eqs/fix_wall_harmonic.jpg)
 
+For style {wall/morse}, the energy E is given by a Morse potential:
+
+:c,image(Eqs/pair_morse.jpg)
+
 In all cases, {r} is the distance from the particle to the wall at
 position {coord}, and Rc is the {cutoff} distance at which the
 particle and wall no longer interact.  The energy of the wall
@@ -147,7 +167,13 @@ constant K, and has units (energy/distance^2).  The input parameter
 spring is at the {cutoff}.  This is a repulsive-only spring since the
 interaction is truncated at the {cutoff}
 
-For any wall, the {epsilon} and/or {sigma} parameter can be specified
+For the {wall/morse} style, the three parameters are in this order:
+{D_0} the depth of the potential, {alpha} the width parameter, and
+{r_0} the location of the minimum.  {D_0} has energy units, {alpha}
+inverse distance units, and {r_0} distance units.
+
+For any wall, the {epsilon} and/or {sigma} and/or {alpha} parameter can
+be specified
 as an "equal-style variable"_variable.html, in which case it should be
 specified as v_name, where name is the variable name.  As with a
 variable wall position, the variable is evaluated each timestep and
diff --git a/doc/src/fix_wall_region.txt b/doc/src/fix_wall_region.txt
index 559a2f0d89..702ca8e694 100644
--- a/doc/src/fix_wall_region.txt
+++ b/doc/src/fix_wall_region.txt
@@ -10,19 +10,27 @@ fix wall/region command :h3
 
 [Syntax:]
 
-fix ID group-ID wall/region region-ID style epsilon sigma cutoff :pre
+fix ID group-ID wall/region region-ID style args ... cutoff :pre
 
-ID, group-ID are documented in "fix"_fix.html command
-wall/region = style name of this fix command
-region-ID = region whose boundary will act as wall
-style = {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic}
-epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
-sigma = size factor for wall-particle interaction (distance units)
-cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :ul
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+wall/region = style name of this fix command :l
+region-ID = region whose boundary will act as wall :l
+style = {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} or {morse} :l
+args for styles {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} = :l
+   epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
+   sigma = size factor for wall-particle interaction (distance units) :pre
+args for style {morse} = :l
+   D_0 = depth of the potential (energy units)
+   alpha = width parameter (1/distance units)
+   r_0 = distance of the potential minimum from wall position (distance units) :pre
+cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :l
+:ule
 
 [Examples:]
 
-fix wall all wall/region mySphere lj93 1.0 1.0 2.5 :pre
+fix wall all wall/region mySphere lj93 1.0 1.0 2.5
+fix wall all wall/region mySphere harmonic 1.0 0.0 2.5
+fix wall all wall/region box_top morse 1.0 1.0 1.5 3.0 :pre
 
 [Description:]
 
@@ -122,15 +130,22 @@ the "pair_style colloid"_pair_colloid.html potential:
 :c,image(Eqs/fix_wall_colloid.jpg)
 
 For style {wall/harmonic}, the energy E is given by a harmonic spring
-potential:
+potential (the distance parameter is ignored):
 
 :c,image(Eqs/fix_wall_harmonic.jpg)
 
+For style {wall/morse}, the energy E is given by the Morse potential:
+
+:c,image(Eqs/pair_morse.jpg)
+
+Unlike other styles, this requires three parameters ({D_0}, {alpha}, {r_0}
+in this order) instead of two like for the other wall styles.
+
 In all cases, {r} is the distance from the particle to the region
 surface, and Rc is the {cutoff} distance at which the particle and
-surface no longer interact.  The energy of the wall potential is
-shifted so that the wall-particle interaction energy is 0.0 at the
-cutoff distance.
+surface no longer interact.  The cutoff is always the last argument.
+The energy of the wall potential is shifted so that the wall-particle
+interaction energy is 0.0 at the cutoff distance.
 
 For a full description of these wall styles, see fix_style
 "wall"_fix_wall.html
@@ -179,7 +194,9 @@ option for this fix.
 
 "fix wall/lj93"_fix_wall.html,
 "fix wall/lj126"_fix_wall.html,
+"fix wall/lj1043"_fix_wall.html,
 "fix wall/colloid"_fix_wall.html,
+"fix wall/harmonic"_fix_wall.html,
 "fix wall/gran"_fix_wall_gran.html
 
 [Default:] none
diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt
new file mode 100644
index 0000000000..47beb776a1
--- /dev/null
+++ b/doc/src/kim_commands.txt
@@ -0,0 +1,522 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+kim_init command :h3
+kim_interactions command :h3
+kim_query command :h3
+
+[Syntax:]
+
+kim_init model user_units unitarg
+kim_interactions typeargs
+kim_query variable formatarg query_function queryargs :pre
+
+model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM)
+user_units = the LAMMPS "units"_units.html style assumed in the LAMMPS input script
+unitarg = {unit_conversion_mode} (optional)
+typeargs = atom type to species mapping (one entry per atom type) or {fixed_types} for models with a preset fixed mapping
+variable = name of a (string style) variable where the result of the query is stored
+formatarg = {split} (optional)
+query_function = name of the OpenKIM web API query function to be used
+queryargs = a series of {keyword=value} pairs that represent the web query; supported keywords depend on the query function :ul
+
+
+[Examples:]
+
+kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
+kim_interactions Si
+kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
+kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode
+kim_interactions C H O
+Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolvents Polymers__SM_039297821658_000 real
+kim_interactions fixed_types
+kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] :pre
+
+[Description:]
+
+The set of {kim_commands} provide a high-level wrapper around the
+"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org
+repository of interatomic models (IMs) (potentials and force fields),
+so that they can be used by LAMMPS scripts.  These commands do not implement
+any computations directly, but rather generate LAMMPS input commands based
+on the information retrieved from the OpenKIM repository to initialize and
+activate OpenKIM IMs and query their predictions for use in the LAMMPS script.
+All LAMMPS input commands generated and executed by {kim_commands} are
+echoed to the LAMMPS log file.
+
+Benefits of Using OpenKIM IMs :h4
+
+Employing OpenKIM IMs provides LAMMPS users with multiple benefits:
+
+Reliability :h5
+
+All content archived in OpenKIM is reviewed by the "KIM Editor"_https://openkim.org/governance/ for quality.
+IMs in OpenKIM are archived with full provenance control. Each is associated with a maintainer responsible for the integrity of the content. All changes are tracked and recorded.
+IMs in OpenKIM are exhaustively tested using "KIM Tests"_https://openkim.org/doc/evaluation/kim-tests/ that compute a host of material properties, and "KIM Verification Checks"_https://openkim.org/doc/evaluation/kim-verification-checks/ that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM's page accessible through the  "OpenKIM browse interface"_https://openkim.org/browse. :ul
+
+Reproducibility :h5
+
+Each IM in OpenKIM is issued a unique identifier ("KIM ID"_https://openkim.org/doc/schema/kim-ids/), which includes a version number (last three digits).  Any changes that can result in different numerical values lead to a version increment in the KIM ID. This makes it possible to reproduce simulations since the specific version of a specific IM used can be retrieved using its KIM ID.
+OpenKIM is a member organization of "DataCite"_https://datacite.org/ and issues digital object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility. :ul
+
+Convenience :h5
+
+IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the {kim_init} command documented on this page.
+The {kim_query} web query tool provides the ability to use the predictions of IMs for supported material properties (computed via "KIM Tests"_https://openkim.org/doc/evaluation/kim-tests/) as part of a LAMMPS input script setup and analysis.
+Support is provided for unit conversion between the "unit style"_units.html used in the LAMMPS input script and the units required by the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the likelihood of errors due to incompatible units.  :ul
+
+:link(IM_types)
+Types of IMs in OpenKIM :h4
+
+There are two types of IMs archived in OpenKIM:
+
+The first type is called a {KIM Portable Model} (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran) that conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see "complete list of supported codes"_https://openkim.org/projects-using-kim/).
+The second type is called a {KIM Simulator Model} (SM). A KIM SM is an IM that is implemented natively within a simulation code ({simulator}) that supports the KIM API Simulator Model Interface (SMI); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol
+
+With these two IM types, OpenKIM can archive and test almost all IMs that
+can be used by LAMMPS. (It is easy to contribute new IMs to OpenKIM, see
+the "upload instructions"_https://openkim.org/doc/repository/adding-content/.)
+
+OpenKIM IMs are uniquely identified by a
+"KIM ID"_https://openkim.org/doc/schema/kim-ids/.
+The extended KIM ID consists of
+a human-readable prefix identifying the type of IM, authors, publication year,
+and supported species, separated by two underscores from the KIM ID itself,
+which begins with an IM code
+({MO} for a KIM Portable Model, and {SM} for a KIM Simulator Model)
+followed by a unique 12-digit code and a 3-digit version identifier.
+By convention SM prefixes begin with {Sim_} to readily identify them.
+
+SW_StillingerWeber_1985_Si__MO_405512056662_005
+Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 :pre
+
+Each OpenKIM IM has a dedicated "Model Page" on "OpenKIM"_https://openkim.org
+providing all the information on the IM including a title, description,
+authorship and citation information, test and verification check results,
+visualizations of results, a wiki with documentation and user comments, and
+access to raw files, and other information.
+The URL for the Model Page is constructed from the
+"extended KIM ID"_https://openkim.org/doc/schema/kim-ids/ of the IM:
+
+https://openkim.org/id/extended_KIM_ID
+:pre
+
+For example for the Stillinger-Weber potential
+listed above the Model Page is located at:
+
+"https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005
+:pre
+
+See the "current list of KIM PMs and SMs archived in OpenKIM"_https://openkim.org/browse/models/by-species.
+This list is sorted by species and can be filtered to display only
+IMs for certain species combinations.
+
+See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to
+learn how to install a pre-build binary of the OpenKIM Repository of Models.
+
+NOTE: It is also possible to locally install IMs not archived in OpenKIM,
+in which case their names do not have to conform to the KIM ID format.
+
+Using OpenKIM IMs with LAMMPS :h4
+
+Two commands are employed when using OpenKIM IMs, one to select the
+IM and perform necessary initialization ({kim_init}), and the second
+to set up the IM for use by executing any necessary LAMMPS commands
+({kim_interactions}). Both are required.
+
+See the {examples/kim} directory for example input scripts that use KIM PMs
+and KIM SMs.
+
+OpenKIM IM Initialization ({kim_init}) :h5
+
+The {kim_init} mode command must be issued [before]
+the simulation box is created (normally at the top of the file).
+This command sets the OpenKIM IM that will be used and may issue
+additional commands changing LAMMPS default settings that are required
+for using the selected IM (such as "units"_units.html or
+"atom_style"_atom_style.html). If needed, those settings can be overridden,
+however, typically a script containing a {kim_init} command
+would not include {units} and {atom_style} commands.
+
+The required arguments of {kim_init} are the {model} name of the
+IM to be used in the simulation (for an IM archived in OpenKIM this is
+its "extended KIM ID"_https://openkim.org/doc/schema/kim-ids/, and
+the {user_units}, which are the LAMMPS "units style"_units.html used
+in the input script.  (Any dimensioned numerical values in the input
+script and values read in from files are expected to be in the
+{user_units} system.)
+
+The selected IM can be either a "KIM PM or a KIM SM"_#IM_types.
+For a KIM SM, the {kim_init} command verifies that the SM is designed
+to work with LAMMPS (and not another simulation code).
+In addition, the LAMMPS version used for defining
+the SM and the LAMMPS version being currently run are
+printed to help diagnose any incompatible changes to input script or
+command syntax between the two LAMMPS versions.
+
+Based on the selected model {kim_init} may modify the
+"atom_style"_atom_style.html.
+Some SMs have requirements for this setting. If this is the case, then
+{atom_style} will be set to the required style. Otherwise, the value is left
+unchanged (which in the absence of an {atom_style} command in the input script
+is the "default atom_style value"_atom_style.html).
+
+Regarding units, the {kim_init} command behaves in different ways depending
+on whether or not {unit conversion mode} is activated as indicated by the
+optional {unitarg} argument.
+If unit conversion mode is [not] active, then {user_units} must
+either match the required units of the IM or the IM must be able
+to adjust its units to match. (The latter is only possible with some KIM PMs;
+SMs can never adjust their units.) If a match is possible, the LAMMPS
+"units"_units.html command is called to set the units to
+{user_units}. If the match fails, the simulation is terminated with
+an error.
+
+Here is an example of a LAMMPS script to compute the cohesive energy
+of a face-centered cubic (fcc) lattice for the Ercolessi and Adams (1994)
+potential for Al:
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+boundary         p p p
+lattice          fcc 4.032
+region           simbox block 0 1 0 1 0 1 units lattice
+create_box       1 simbox
+create_atoms     1 box
+mass             1 26.981539
+kim_interactions Al
+run              0
+variable         Ec equal (pe/count(all))/$\{_u_energy\}
+print            "Cohesive Energy = $\{EcJ\} eV"
+:pre
+
+The above script will end with an error in the {kim_init} line if the
+IM is changed to another potential for Al that does not work with {metal}
+units. To address this {kim_init} offers the {unit_conversion_mode}.
+If unit conversion mode {is} active, then {kim_init} calls the LAMMPS
+"units"_units.html command to set the units to the IM's required or
+preferred units. Conversion factors between the IM's units and the {user_units}
+are defined for all "physical quantities"_units.html (mass, distance, etc.).
+(Note that converting to or from the "lj" unit style is not supported.)
+These factors are stored as "internal style variables"_variable.html with
+the following standard names:
+
+_u_mass
+_u_distance
+_u_time
+_u_energy
+_u_velocity
+_u_force
+_u_torque
+_u_temperature
+_u_pressure
+_u_viscosity
+_u_charge
+_u_dipole
+_u_efield
+_u_density :pre
+
+If desired, the input script can be designed to work with these conversion
+factors so that the script will work without change with any OpenKIM IM.
+(This approach is used in the
+"OpenKIM Testing Framework"_https://openkim.org/doc/evaluation/kim-tests/.)
+For example, the script given above for the cohesive energy of fcc Al
+can be rewritten to work with any IM regardless of units. The following
+script constructs an fcc lattice with a lattice parameter defined in
+meters, computes the total energy, and prints the cohesive energy in
+Joules regardless of the units of the IM.
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 si unit_conversion_mode
+boundary         p p p
+lattice          fcc 4.032e-10*$\{_u_distance\}
+region           simbox block 0 1 0 1 0 1 units lattice
+create_box       1 simbox
+create_atoms     1 box
+mass             1 4.480134e-26*$\{_u_mass\}
+kim_interactions Al
+run              0
+variable         Ec_in_J equal (pe/count(all))/$\{_u_energy\}
+print            "Cohesive Energy = $\{Ec_in_J\} J" :pre
+
+Note the multiplication by $\{_u_distance\} and $\{_u_mass\} to convert
+from SI units (specified in the {kim_init} command) to whatever units the
+IM uses (metal in this case), and the division by $\{_u_energy\}
+to convert from the IM's energy units to SI units (Joule). This script
+will work correctly for any IM for Al (KIM PM or SM) selected by the
+{kim_init} command.
+
+Care must be taken to apply unit conversion to dimensional variables read in
+from a file. For example if a configuration of atoms is read in from a
+dump file using the "read_dump"_read_dump.html command, the following can
+be done to convert the box and all atomic positions to the correct units:
+
+variable xyfinal equal xy*$\{_u_distance\}
+variable xzfinal equal xz*$\{_u_distance\}
+variable yzfinal equal yz*$\{_u_distance\}
+change_box all x scale $\{_u_distance\} &
+                       y scale $\{_u_distance\} &
+                       z scale $\{_u_distance\} &
+                       xy final $\{xyfinal\} &
+                       xz final $\{xzfinal\} &
+                       yz final $\{yzfinal\} &
+                       remap  :pre
+
+NOTE: Unit conversion will only work if the conversion factors are placed in
+all appropriate places in the input script. It is up to the user to do this
+correctly.
+
+OpenKIM IM Execution ({kim_interactions}) :h5
+
+The second and final step in using an OpenKIM IM is to execute the
+{kim_interactions} command. This command must be preceded by a {kim_init}
+command and a command that defines the number of atom types {N} (such as
+"create_box"_create_box.html).
+The {kim_interactions} command has one argument {typeargs}. This argument
+contains either a list of {N} chemical species, which defines a mapping between
+atom types in LAMMPS to the available species in the OpenKIM IM, or the
+keyword {fixed_types} for models that have a preset fixed mapping (i.e.
+the mapping between LAMMPS atom types and chemical species is defined by
+the model and cannot be changed). In the latter case, the user must consult
+the model documentation to see how many atom types there are and how they
+map to the chemical species.
+
+For example, consider an OpenKIM IM that supports Si and C species.
+If the LAMMPS simulation has four atom types, where the first three are Si,
+and the fourth is C, the following {kim_interactions} command would be used:
+
+kim_interactions Si Si Si C
+:pre
+
+Alternatively, for a model with a fixed mapping the command would be:
+
+kim_interactions fixed_types
+:pre
+
+The {kim_interactions} command performs all the necessary steps to set up
+the OpenKIM IM selected in the {kim_init} command. The specific actions depend
+on whether the IM is a KIM PM or a KIM SM.  For a KIM PM,
+a "pair_style kim"_pair_kim.html command is executed followed by
+the appropriate {pair_coeff} command. For example, for the
+Ercolessi and Adams (1994) KIM PM for Al set by the following commands:
+
+kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+...
+...  box specification lines skipped
+...
+kim_interactions Al :pre
+
+the {kim_interactions} command executes the following LAMMPS input commands:
+
+pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005
+pair_coeff * * Al  :pre
+
+For a KIM SM, the generated input commands may be more complex
+and require that LAMMPS is built with the required packages included
+for the type of potential being used. The set of commands to be executed
+is defined in the SM specification file, which is part of the SM package.
+For example, for the Strachan et al. (2003) ReaxFF SM
+set by the following commands:
+
+kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
+...
+...  box specification lines skipped
+...
+kim_interactions C H N O  :pre
+
+the {kim_interactions} command executes the following LAMMPS input commands:
+
+pair_style reax/c lmp_control safezone 2.0 mincap 100
+pair_coeff * * ffield.reax.rdx C H N O
+fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq  :pre
+
+Note that the files {lmp_control}, {ffield.reax.rdx} and {param.qeq}
+are specific to the Strachan et al. (2003) ReaxFF parameterization
+and are archived as part of the SM package in OpenKIM.
+Note also that parameters like cutoff radii and charge tolerances,
+which have an effect on IM predictions, are also included in the
+SM definition ensuring reproducibility.
+
+NOTE: When using {kim_init} and {kim_interactions} to select
+and set up an OpenKIM IM, other LAMMPS commands
+for the same functions (such as pair_style, pair_coeff, bond_style,
+bond_coeff, fixes related to charge equilibration, etc.) should normally
+not appear in the input script.
+
+Using OpenKIM Web Queries in LAMMPS ({kim_query}) :h5
+
+The {kim_query} command performs a web query to retrieve the predictions
+of the IM set by {kim_init} for material properties archived in
+"OpenKIM"_https://openkim.org.  The {kim_query} command must be preceded
+by a {kim_init} command. The result of the query is stored in a
+"string style variable"_variable.html, the name of which is given as the first
+argument of the {kim_query command}.  (For the case of multiple
+return values, the optional {split} keyword can be used after the
+variable name to separate the results into multiple variables; see
+the "example"_#split_example below.)
+The second required argument {query_function} is the name of the
+query function to be called (e.g. {get_lattice_constant_cubic}).
+All following "arguments"_Commands_parse.html are parameters handed over to
+the web query in the format {keyword=value}, where {value} is always
+an array of one or more comma-separated items in brackets.
+The list of supported keywords and the type and format of their values
+depend on the query function used. The current list of query functions
+is available on the OpenKIM webpage at
+"https://openkim.org/doc/usage/kim-query"_https://openkim.org/doc/usage/kim-query.
+
+NOTE: All query functions require the {model} keyword, which identifies
+the IM whose predictions are being queried. This keyword is automatically
+generated by {kim_query} based on the IM set in {kim_init} and must not
+be specified as an argument to {kim_query}.
+
+NOTE: Each {query_function} is associated with a default method (implemented
+as a "KIM Test"_https://openkim.org/doc/evaluation/kim-tests/)
+used to compute this property. In cases where there are multiple
+methods in OpenKIM for computing a property, a {method} keyword can
+be provided to select the method of choice.  See the
+"query documentation"_https://openkim.org/doc/repository/kim-query
+to see which methods are available for a given {query function}.
+
+{kim_query} Usage Examples and Further Clarifications: :h6
+
+The data obtained by {kim_query} commands can be used as part of the setup
+or analysis phases of LAMMPS simulations. Some examples are given below.
+
+[Define an equilibrium fcc crystal]
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+boundary         p p p
+kim_query        a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\]
+lattice          fcc $\{a0\}
+... :pre
+
+The {kim_query} command retrieves from "OpenKIM"_https://openkim.org
+the equilibrium lattice constant predicted by the Ercolessi and Adams (1994)
+potential for the fcc structure and places it in
+variable {a0}. This variable is then used on the next line to set up the
+crystal. By using {kim_query}, the user is saved the trouble and possible
+error of tracking this value down, or of having to perform an energy
+minimization to find the equilibrium lattice constant.
+
+Note that in {unit_conversion_mode} the results obtained from a
+{kim_query} would need to be converted to the appropriate units system.
+For example, in the above script, the lattice command would need to be
+changed to: "lattice fcc $\{a0\}*$\{_u_distance\}".
+
+:link(split_example)
+[Define an equilibrium hcp crystal]
+
+kim_init         EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal
+boundary         p p p
+kim_query        latconst split get_lattice_constant_hexagonal crystal=\["hcp"\] species=\["Zr"\] units=\["angstrom"\]
+variable         a0 equal latconst_1
+variable         c0 equal latconst_2
+variable         c_to_a equal $\{c0\}/$\{a0\}
+lattice          custom $\{a0\} a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 $\{c_to_a\} &
+                 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75
+... :pre
+
+In this case the {kim_query} returns two arguments (since the hexagonal
+close packed (hcp) structure has two independent lattice constants).
+The default behavior of {kim_query} returns the result as a string
+with the values separated by commas. The optional keyword {split}
+separates the result values into individual variables of the form
+{prefix_I}, where {prefix} is set to the the {kim_query} {variable} argument
+and {I} ranges from 1 to the number of returned values. The number and order of
+the returned values is determined by the type of query performed.
+
+[Define a crystal at finite temperature accounting for thermal expansion]
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+boundary         p p p
+kim_query        a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\]
+kim_query        alpha get_linear_thermal_expansion_coefficient_cubic  crystal=\["fcc"\] species=\["Al"\] units=\["1/K"\] temperature=\[293.15\] temperature_units=\["K"\]
+variable         DeltaT equal 300
+lattice          fcc $\{a0\}*$\{alpha\}*$\{DeltaT\}
+... :pre
+
+As in the previous example, the equilibrium lattice constant is obtained
+for the Ercolessi and Adams (1994) potential. However, in this case the
+crystal is scaled to the appropriate lattice constant at room temperature
+(293.15 K) by using the linear thermal expansion constant predicted by the
+potential.
+
+NOTE: When passing numerical values as arguments (as in the case
+of the temperature in the above example) it is also possible to pass a
+tolerance indicating how close to the value is considered a match.
+If no tolerance is passed a default value is used. If multiple results
+are returned (indicating that the tolerance is too large), {kim_query}
+will return an error. See the
+"query documentation"_https://openkim.org/doc/repository/kim-query
+to see which numerical arguments and tolerances are available for a
+given {query function}.
+
+[Compute defect formation energy]
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+...
+... Build fcc crystal containing some defect and compute the total energy
+... which is stored in the variable {Etot}
+...
+kim_query        Ec get_cohesive_energy_cubic crystal=\["fcc"\] species=\["Al"\] units=\["eV"\]
+variable         Eform equal $\{Etot\} - count(all)*$\{Ec\}
+... :pre
+
+The defect formation energy {Eform} is computed by subtracting from {Etot} the
+ideal fcc cohesive energy of the atoms in the system obtained from
+"OpenKIM"_https://openkim.org for the Ercolessi and Adams (1994) potential.
+
+NOTE: {kim_query} commands return results archived in
+"OpenKIM"_https://openkim.org. These results are obtained
+using programs for computing material properties
+(KIM Tests and KIM Test Drivers) that were contributed to OpenKIM.
+In order to give credit to Test developers, the number of times results
+from these programs are queried is tracked. No other information about
+the nature of the query or its source is recorded.
+
+
+Citation of OpenKIM IMs :h4
+
+When publishing results obtained using OpenKIM IMs researchers are requested
+to cite the OpenKIM project "(Tadmor)"_#kim-mainpaper, KIM API
+"(Elliott)"_#kim-api, and the specific IM codes used in the simulations,
+in addition to the relevant scientific references for the IM.
+The citation format for an IM is displayed on its page on
+"OpenKIM"_https://openkim.org along with the corresponding BibTex file,
+and is automatically added to the LAMMPS {log.cite} file.
+
+Citing the IM software (KIM infrastructure and specific PM or SM codes)
+used in the simulation gives credit to the researchers who developed them
+and enables open source efforts like OpenKIM to function.
+
+
+[Restrictions:]
+
+The set of {kim_commands} is part of the KIM package.  It is only enabled if
+LAMMPS is built with that package. A requirement for the KIM package,
+is the KIM API library that must be downloaded from the
+"OpenKIM website"_https://openkim.org/kim-api/ and installed before
+LAMMPS is compiled. When installing LAMMPS from binary, the kim-api package
+is a dependency that is automatically downloaded and installed. See the KIM
+section of the "Packages details"_Packages_details.html for details.
+
+Furthermore, when using {kim_commands} to run KIM SMs, any packages required
+by the native potential being used or other commands or fixes that it invokes
+must be installed.
+
+[Related commands:]
+
+"pair_style kim"_pair_kim.html
+
+:line
+
+:link(kim-mainpaper)
+[(Tadmor)] Tadmor, Elliott, Sethna, Miller and Becker, JOM, 63, 17 (2011).
+doi: "https://doi.org/10.1007/s11837-011-0102-6"_https://doi.org/10.1007/s11837-011-0102-6
+
+:link(kim-api)
+[(Elliott)] Elliott, Tadmor and Bernstein, "https://openkim.org/kim-api"_https://openkim.org/kim-api (2011)
+doi: "https://doi.org/10.25950/FF8F563A"_https://doi.org/10.25950/FF8F563A
diff --git a/doc/src/kim_query.txt b/doc/src/kim_query.txt
deleted file mode 100644
index c581de0ebb..0000000000
--- a/doc/src/kim_query.txt
+++ /dev/null
@@ -1,46 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-kim_query command :h3
-
-[Syntax:]
-
-kim_query variable query_function web_query_flags :pre
-
-variable = name of a (string style) variable where the result of the query is stored
-query_function = name of the OpenKIM web API query function to be used
-web_query_flags = a series of keyword=value pairs that represent the web query; supported keywords depend on query function :ul
-
-[Examples:]
-
-kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 &
-  prop=structure-cubic-crystal-npt species=\["Al"\] keys=\["a"\] units=\["angstrom"\] :pre
-
-[Description:]
-
-The kim_query command allows to retrieve properties from the OpenKIM
-through a web query. The result is stored in a string style
-"variable"_variable.html, the name of which must be given as the first
-argument of the kim_query command.  The second required argument is the
-name of the actual query function (e.g. {get_test_result}).  All following
-arguments are parameters handed over to the web query in the format
-{keyword=value}.  The list of supported keywords and the type of how
-the value has to be encoded depends on the query function used.  This
-mirrors the functionality available on the OpenKIM webpage at
-"https://query.openkim.org"_https://query.openkim.org/
-
-[Restrictions:]
-
-This command is part of the KIM package.  It is only enabled if
-LAMMPS was built with that package.  Furthermore, its correct
-functioning depends on compiling LAMMPS with libcurl support.
-See the "Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"pair_style kim"_pair_kim.html, "variable"_variable.html
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 8abe9cffa1..3c856bde19 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -42,6 +42,7 @@ Commands_compute.html
 Commands_pair.html
 Commands_bond.html
 Commands_kspace.html
+Commands_removed.html
 Packages.html
 Packages_standard.html
 Packages_user.html
@@ -167,7 +168,7 @@ if.html
 include.html
 info.html
 jump.html
-kim_query.html
+kim_commands.html
 label.html
 lattice.html
 log.html
@@ -455,6 +456,7 @@ compute_global_atom.html
 compute_group_group.html
 compute_gyration.html
 compute_gyration_chunk.html
+compute_gyration_shape.html
 compute_heat_flux.html
 compute_hexorder_atom.html
 compute_improper.html
@@ -468,6 +470,7 @@ compute_ke_rigid.html
 compute_meso_e_atom.html
 compute_meso_rho_atom.html
 compute_meso_t_atom.html
+compute_momentum.html
 compute_msd.html
 compute_msd_chunk.html
 compute_msd_nongauss.html
@@ -566,6 +569,7 @@ pair_charmm.html
 pair_class2.html
 pair_colloid.html
 pair_comb.html
+pair_cosine_squared.html
 pair_coul.html
 pair_coul_diel.html
 pair_coul_shield.html
diff --git a/doc/src/min_style.txt b/doc/src/min_style.txt
index c46c1492b4..e27682cf97 100644
--- a/doc/src/min_style.txt
+++ b/doc/src/min_style.txt
@@ -11,7 +11,7 @@ min_style command :h3
 
 min_style style :pre
 
-style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul
+style = {cg} or {cg/kk} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul
 
 [Examples:]
 
@@ -74,9 +74,34 @@ defined via the "timestep"_timestep.html command.  Often they will
 converge more quickly if you use a timestep about 10x larger than you
 would normally use for dynamics simulations.
 
-NOTE: The {quickmin}, {fire}, and {hftn} styles do not yet support the
-use of the "fix box/relax"_fix_box_relax.html command or minimizations
-involving the electron radius in "eFF"_pair_eff.html models.
+NOTE: The {quickmin}, {fire}, {hftn}, and {cg/kk} styles do not yet 
+support the use of the "fix box/relax"_fix_box_relax.html command or 
+minimizations involving the electron radius in "eFF"_pair_eff.html 
+models. 
+
+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
 
 [Restrictions:] none
 
diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt
index ecf1ad0fcf..42315705e5 100644
--- a/doc/src/minimize.txt
+++ b/doc/src/minimize.txt
@@ -7,6 +7,7 @@
 :line
 
 minimize command :h3
+minimize/kk command :h3
 
 [Syntax:]
 
@@ -256,6 +257,28 @@ info in the Restrictions section below.
 
 :line
 
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 Features that are not yet implemented are listed here, in case someone
diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt
index fc888ffbff..de6717a6c3 100644
--- a/doc/src/pair_adp.txt
+++ b/doc/src/pair_adp.txt
@@ -42,16 +42,17 @@ the ADP potential files themselves.  Likewise, the ADP potential files
 list atomic masses; thus you do not need to use the "mass"_mass.html
 command to specify them.
 
-The NIST WWW site distributes and documents ADP potentials:
+[ADP potentials are available from:]
 
-http://www.ctcms.nist.gov/potentials :pre
+The NIST WWW site at http://www.ctcms.nist.gov/potentials.
+Note that ADP potentials obtained from NIST must be converted
+into the extended DYNAMO {setfl} format discussed below.
+:l
 
-Note that these must be converted into the extended DYNAMO {setfl}
-format discussed below.
-
-The NIST site is maintained by Chandler Becker (cbecker at nist.gov)
-who is good resource for info on interatomic potentials and file
-formats.
+The OpenKIM Project at https://openkim.org/browse/models/by-type provides
+ADP potentials that can be used directly in LAMMPS with the "kim_commands
+interface"_kim_commands.html.
+:l
 
 :line
 
diff --git a/doc/src/pair_cosine_squared.txt b/doc/src/pair_cosine_squared.txt
new file mode 100644
index 0000000000..f60e33f70d
--- /dev/null
+++ b/doc/src/pair_cosine_squared.txt
@@ -0,0 +1,108 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+pair_style cosine/squared command :h3
+
+[Syntax:]
+
+pair_style cosine/squared cutoff :pre
+
+cutoff = global cutoff for cosine-squared interactions (distance units) :ul
+
+pair_coeff i j eps sigma
+pair_coeff i j eps sigma cutoff
+pair_coeff i j eps sigma wca
+pair_coeff i j eps sigma cutoff wca :pre
+
+i,j = a particle type
+eps = interaction strength, i.e. the depth of the potential minimum (energy units)
+sigma = distance of the potential minimum from 0
+cutoff = the cutoff distance for this pair type, if different from global (distance units)
+wca = if specified a Weeks-Chandler-Andersen potential (with eps strength and minimum at sigma) is added, otherwise not :ul
+
+[Examples:]
+
+pair_style cosine/squared 3.0
+pair_coeff * * 1.0 1.3
+pair_coeff 1 3 1.0 1.3 2.0
+pair_coeff 1 3 1.0 1.3 wca
+pair_coeff 1 3 1.0 1.3 2.0 wca :pre
+
+[Description:]
+
+Style {cosine/squared} computes a potential of the form
+
+:c,image(Eqs/pair_cosine_squared.jpg)
+
+between two point particles, where (sigma, -epsilon) is the location of
+the (rightmost) minimum of the potential, as explained in the syntax
+section above.
+
+This potential was first used in (Cooke)_#CKD for a coarse-grained lipid
+membrane model.  It is generally very useful as a non-specific
+interaction potential because it is fully adjustable in depth and width
+while joining the minimum at (sigma, -epsilon) and zero at (cutoff, 0)
+smoothly, requiring no shifting and causing no related artifacts, tail
+energy calculations etc. This evidently requires {cutoff} to be larger
+than {sigma}.
+
+If the {wca} option is used then a Weeks-Chandler-Andersen potential
+(Weeks)_#WCA is added to the above specified cosine-squared potential,
+specifically the following:
+
+:c,image(Eqs/pair_cosine_squared_wca.jpg)
+
+In this case, and this case only, the {sigma} parameter can be equal to
+{cutoff} (sigma = cutoff) which will result in ONLY the WCA potential
+being used (and print a warning), so the minimum will be attained at
+(sigma, 0). This is a convenience feature that enables a purely
+repulsive potential to be used without a need to define an additional
+pair style and use the hybrid styles.
+
+The energy and force of this pair style for parameters epsilon = 1.0,
+sigma = 1.0, cutoff = 2.5, with and without the WCA potential, are shown
+in the graphs below:
+
+:c,image(JPG/pair_cosine_squared_graphs.jpg)
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+Mixing is not supported for this style.
+
+The {shift}, {table} and {tail} options are not relevant for this style.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+These pair styles can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command.  They do not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+The {cosine/squared} style is part of the "USER-MISC" package. It is only
+enabled if LAMMPS is build with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html,
+"pair_style lj/cut"_pair_lj.html
+
+[Default:] none
+
+:link(CKD)
+[(Cooke)] "Cooke, Kremer and Deserno, Phys. Rev. E, 72, 011506 (2005)"
+
+:link(WCA)
+[(Weeks)] "Weeks, Chandler and Andersen, J. Chem. Phys., 54, 5237 (1971)"
diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt
index df04e76de9..8152a1a12e 100644
--- a/doc/src/pair_coul_shield.txt
+++ b/doc/src/pair_coul_shield.txt
@@ -13,7 +13,7 @@ pair_style coul/shield command :h3
 pair_style coul/shield cutoff tap_flag :pre
 
 cutoff = global cutoff (distance units)
-tap_flag = 0/1 to turn off/on the taper function
+tap_flag = 0/1 to turn off/on the taper function :ul
 
 [Examples:]
 
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt
index 4dd244c17f..6d922e20f9 100644
--- a/doc/src/pair_ilp_graphene_hbn.txt
+++ b/doc/src/pair_ilp_graphene_hbn.txt
@@ -13,17 +13,17 @@ pair_style ilp/graphene/hbn command :h3
 pair_style \[hybrid/overlay ...\] ilp/graphene/hbn cutoff tap_flag :pre
 
 cutoff = global cutoff (distance units)
-tap_flag = 0/1 to turn off/on the taper function
+tap_flag = 0/1 to turn off/on the taper function :ul
 
 [Examples:]
 
-pair_style hybrid/overlay ilp/graphene/hbn 16.0 1
-pair_coeff * * ilp/graphene/hbn  BNCH.ILP B N C :pre
+pair_style  hybrid/overlay ilp/graphene/hbn 16.0 1
+pair_coeff  * * ilp/graphene/hbn  BNCH.ILP B N C :pre
 
 pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
-pair_coeff  * * rebo                 CH.rebo     NULL NULL C
-pair_coeff  * * tersoff              BNC.tersoff B    N    NULL
-pair_coeff  * * ilp/graphene/hbn     BNCH.ILP    B    N    C
+pair_coeff  * * rebo              CH.rebo     NULL NULL C
+pair_coeff  * * tersoff           BNC.tersoff B    N    NULL
+pair_coeff  * * ilp/graphene/hbn  BNCH.ILP    B    N    C
 pair_coeff  1 1 coul/shield 0.70
 pair_coeff  1 2 coul/shield 0.695
 pair_coeff  2 2 coul/shield 0.69 :pre
@@ -85,6 +85,22 @@ be found in "(Ouyang)"_#Ouyang.
 This potential must be used in combination with hybrid/overlay.
 Other interactions can be set to zero using pair_style {none}.
 
+This pair style tallies a breakdown of the total interlayer potential
+energy into sub-categories, which can be accessed via the "compute
+pair"_compute_pair.html command as a vector of values of length 2.
+The 2 values correspond to the following sub-categories:
+
+{E_vdW} = vdW (attractive) energy
+{E_Rep} = Repulsive energy :ol
+
+To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+
+compute 0 all pair ilp/graphene/hbn
+variable Evdw  equal c_0\[1\]
+variable Erep  equal c_0\[2\]
+thermo_style custom step temp epair v_Erep v_Evdw :pre
+
 :line
 
 [Mixing, shift, table, tail correction, restart, rRESPA info]:
diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt
index a415ac606b..41593675ba 100644
--- a/doc/src/pair_kim.txt
+++ b/doc/src/pair_kim.txt
@@ -12,76 +12,72 @@ pair_style kim command :h3
 
 pair_style kim model :pre
 
-model = name of KIM model (potential)
+model = name of a KIM model (the KIM ID for models archived in OpenKIM)
 
 [Examples:]
 
-pair_style kim ex_model_Ar_P_LJ
-pair_coeff * * Ar Ar :pre
+pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
+pair_coeff * * Si :pre
 
 [Description:]
 
-This pair style is a wrapper on the "Knowledge Base for Interatomic
+This pair style is a wrapper on the "Open Knowledgebase of Interatomic
 Models (OpenKIM)"_https://openkim.org repository of interatomic
-potentials, so that they can be used by LAMMPS scripts.
+potentials to enable their use in LAMMPS scripts.
 
-Note that in LAMMPS lingo, a KIM model driver is a pair style
-(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
-element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file.
+The preferred interface for using interatomic models archived in
+OpenKIM is the "kim_commands interface"_kim_commands.html. That
+interface supports both "KIM Portable Models" (PMs) that conform to the
+KIM API Portable Model Interface (PMI) and can be used by any
+simulation code that conforms to the KIM API/PMI, and
+"KIM Simulator Models" that are natively implemented within a single
+simulation code (like LAMMPS) and can only be used with it.
+The {pair_style kim} command is limited to KIM PMs. It is
+used by the "kim_commands interface"_kim_commands.html as needed.
 
-See the current list of "KIM model
-drivers"_https://openkim.org/browse/model-drivers/alphabetical.
+NOTE: Since {pair_style kim} is called by {kim_interactions} as needed,
+is not recommended to be directly used in input scripts.
 
-See the current list of all "KIM
-models"_https://openkim.org/browse/models/by-model-drivers
-
-To use this pair style, you must first download and install the KIM
-API library from the "OpenKIM website"_https://openkim.org.  The KIM
-section of the "Packages details"_Packages_details.html doc page has
-instructions on how to do this with a simple make command, when
-building LAMMPS.
-
-See the examples/kim dir for an input script that uses a KIM model
-(potential) for Lennard-Jones.
- 
 :line
 
-The argument {model} is the name of the KIM model for a specific
-potential as KIM defines it.  In principle, LAMMPS can invoke any KIM
-model.  You should get an error or warning message from either LAMMPS
-or KIM if there is an incompatibility.
+The argument {model} is the name of the KIM PM.
+For potentials archived in OpenKIM
+this is the extended KIM ID (see "kim_commands"_kim_commands.html
+for details). LAMMPS can invoke any KIM PM, however there can
+be incompatibilities (for example due to unit matching issues).
+In the event of an incompatibility, the code will terminate with
+an error message. Check both the LAMMPS and KIM log files for details.
 
-Only a single pair_coeff command is used with the {kim} style which
-specifies the mapping of LAMMPS atom types to KIM elements.  This is
-done by specifying N additional arguments after the * * in the
-pair_coeff command, where N is the number of LAMMPS atom types:
+Only a single {pair_coeff} command is used with the {kim} style, which
+specifies the mapping of LAMMPS atom types to the species supported by
+the KIM PM.  This is done by specifying {N} additional arguments
+after the * * in the {pair_coeff} command, where {N} is the number of
+LAMMPS atom types:
 
 N element names = mapping of KIM elements to atom types :ul
 
-As an example, imagine the KIM model supports Si and C atoms.  If your
-LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si,
-and the 4th to be C, you would use the following pair_coeff command:
+For example, consider a KIM PM that supports Si and C species.
+If the LAMMPS simulation has four atom types, where the first three are Si,
+and the fourth is C, the following {pair_coeff} command would be used:
 
 pair_coeff * * Si Si Si C :pre
 
-The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
-The first three Si arguments map LAMMPS atom types 1,2,3 to Si as
-defined within KIM.  The final C argument maps LAMMPS atom type 4 to C
-as defined within KIM.
+The first two arguments must be * * so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1, 2, and 3 to Si as
+defined within KIM PM.  The final C argument maps LAMMPS atom type 4 to C.
 
 :line
 
 In addition to the usual LAMMPS error messages, the KIM library itself
 may generate errors, which should be printed to the screen.  In this
-case it is also useful to check the kim.log file for additional error
-information.  The file kim.log should be generated in the same
+case it is also useful to check the {kim.log} file for additional error
+information.  The file {kim.log} should be generated in the same
 directory where LAMMPS is running.
 
 To download, build, and install the KIM library on your system, see
-the lib/kim/README file.  Once you have done this and built LAMMPS
+the {lib/kim/README} file.  Once you have done this and built LAMMPS
 with the KIM package installed you can run the example input scripts
-in examples/kim.
+in {examples/kim}.
 
 :line
 
@@ -103,15 +99,14 @@ This pair style can only be used via the {pair} keyword of the
 
 [Restrictions:]
 
-This pair style is part of the KIM package.  It is only enabled if
-LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
+This pair style is part of the KIM package. See details on
+restrictions in "kim_commands"_kim_commands.html.
 
 This current version of pair_style kim is compatible with the
 kim-api package version 2.0.0 and higher.
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html
+"pair_coeff"_pair_coeff.html, "kim_commands"_kim_commands.html
 
 [Default:] none
diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt
index 9ad5bfea84..5a2623ed89 100644
--- a/doc/src/pair_kolmogorov_crespi_full.txt
+++ b/doc/src/pair_kolmogorov_crespi_full.txt
@@ -13,7 +13,7 @@ pair_style kolmogorov/crespi/full command :h3
 pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag :pre
 
 cutoff = global cutoff (distance units)
-tap_flag = 0/1 to turn off/on the taper function
+tap_flag = 0/1 to turn off/on the taper function :ul
 
 [Examples:]
 
@@ -74,6 +74,22 @@ comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
 This potential must be used in combination with hybrid/overlay.
 Other interactions can be set to zero using pair_style {none}.
 
+This pair style tallies a breakdown of the total interlayer potential
+energy into sub-categories, which can be accessed via the "compute
+pair"_compute_pair.html command as a vector of values of length 2.
+The 2 values correspond to the following sub-categories:
+
+{E_vdW} = vdW (attractive) energy
+{E_Rep} = Repulsive energy :ol
+
+To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+
+compute 0 all pair kolmogorov/crespi/full
+variable Evdw  equal c_0\[1\]
+variable Erep  equal c_0\[2\]
+thermo_style custom step temp epair v_Erep v_Evdw :pre
+
 :line
 
 [Mixing, shift, table, tail correction, restart, rRESPA info]:
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index 8a35e5a467..1b8e6d46ec 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -129,6 +129,7 @@ accelerated styles exist.
 "colloid"_pair_colloid.html - integrated colloidal potential
 "comb"_pair_comb.html - charge-optimized many-body (COMB) potential
 "comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential
+"cosine/squared"_pair_cosine_squared.html - Cooke-Kremer-Deserno membrane model potential
 "coul/cut"_pair_coul.html - cutoff Coulombic potential
 "coul/cut/soft"_pair_fep_soft.html - Coulombic potential with a soft core
 "coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index 2f63f18bad..f36a87dea3 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -24,6 +24,7 @@ Pair Styles :h1
    pair_class2
    pair_colloid
    pair_comb
+   pair_cosine_squared
    pair_coul
    pair_coul_diel
    pair_coul_shield
diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt
index 79a481746e..50e6e4c6d2 100644
--- a/doc/src/replicate.txt
+++ b/doc/src/replicate.txt
@@ -14,7 +14,8 @@ replicate nx ny nz {keyword} :pre
 
 nx,ny,nz = replication factors in each dimension :ulb
 optional {keyword} = {bbox} :l
-  {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :ule
+  {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :pre
+:ule
 
 [Examples:]
 
@@ -45,11 +46,13 @@ file that crosses a periodic boundary should be between two atoms with
 image flags that differ by 1.  This will allow the bond to be
 unwrapped appropriately.
 
-The optional keyword {bbox} uses a bounding box to only check atoms
-in replicas that overlap with a processor's sub-domain when assigning
-atoms to processors, and thus can result in substantial speedups for
-calculations using a large number of processors. It does require
-temporarily using more memory.
+The optional keyword {bbox} uses a bounding box to only check atoms in
+replicas that overlap with a processor's sub-domain when assigning
+atoms to processors.  It typically results in a substantial speedup
+when using the replicate command on a large number of processors.  It
+does require temporary use of more memory, specifically that each
+processor can store all atoms in the entire system before it is
+replicated.
 
 [Restrictions:]
 
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index da5c869075..6d5112b4c7 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -20,6 +20,7 @@ acolor
 acos
 Acta
 actinide
+acylindricity
 addforce
 Addington
 addtorque
@@ -44,6 +45,7 @@ Aidan
 aij
 airebo
 Aj
+ajs
 ajaramil
 akohlmey
 Aktulga
@@ -98,6 +100,7 @@ antisymmetry
 anton
 Antonelli
 api
+Apoorva
 Appl
 Apu
 arccos
@@ -113,6 +116,7 @@ askoose
 asphere
 ASPHERE
 aspherical
+asphericity
 Asq
 assignee
 Asta
@@ -354,6 +358,7 @@ Cii
 Cij
 cis
 civ
+CKD
 Clang
 clearstore
 Cleary
@@ -419,6 +424,7 @@ coreshell
 cornflowerblue
 cornsilk
 corotate
+corotation
 corotational
 correlator
 cosineshifted
@@ -481,6 +487,7 @@ cvff
 cwiggle
 cygwin
 Cygwin
+cylindrically
 Cyrot
 cyrstals
 Daivis
@@ -518,6 +525,7 @@ Dcut
 de
 dE
 De
+decorrelation
 debye
 Debye
 Decius
@@ -526,6 +534,7 @@ decrementing
 deeppink
 deepskyblue
 defgrad
+defn
 deformable
 del
 deleteIDs
@@ -574,6 +583,7 @@ Dihedrals
 dihydride
 Dij
 dimdim
+dimensioned
 dimensionality
 dimgray
 dipolar
@@ -603,6 +613,7 @@ Dobson
 Dodds
 dodgerblue
 dof
+doi
 Donadio
 dotc
 Doty
@@ -754,6 +765,7 @@ equilibrating
 equilibration
 Equilibria
 equilization
+Ercolessi
 eradius
 erate
 erc
@@ -880,6 +892,7 @@ Fogarty
 Foiles
 fopenmp
 forestgreen
+formatarg
 formulae
 Forschungszentrum
 Fortran
@@ -1065,6 +1078,7 @@ Hilger
 histo
 histogrammed
 histogramming
+hma
 hmaktulga
 hoc
 Hochbruck
@@ -1321,6 +1335,8 @@ kmax
 Kmax
 Knizhnik
 knl
+Kofke
+kofke
 Kohlmeyer
 Kohn
 kokkos
@@ -1514,6 +1530,7 @@ lz
 Maaravi
 Mackay
 Mackrodt
+Macromolecules
 macroparticle
 Madura
 Magda
@@ -1539,6 +1556,7 @@ Mandelli
 Manh
 manifoldforce
 Manolopoulos
+manpages
 manybody
 MANYBODY
 Maras
@@ -1619,6 +1637,7 @@ meso
 mesoparticle
 mesoscale
 mesoscopic
+metadata
 metadynamics
 Metadynamics
 Methfessel
@@ -1705,6 +1724,7 @@ Morteza
 Mosayebi
 Moseler
 Moskalev
+Moustafa
 mov
 mpi
 MPI
@@ -2204,6 +2224,7 @@ PTM
 ptr
 pu
 purdue
+Purohit
 pushstore
 pvar
 pw
@@ -2257,6 +2278,7 @@ quati
 quatj
 quatk
 quatw
+queryargs
 Queteschiner
 qw
 qx
@@ -2286,6 +2308,7 @@ rcutfac
 rdc
 rdf
 RDideal
+rdx
 README
 realtime
 reamin
@@ -2312,6 +2335,8 @@ Rensselaer
 reparameterizing
 repo
 representable
+Reproducibility
+reproducibility
 repuls
 rescale
 rescaled
@@ -2417,6 +2442,7 @@ Ryckaert
 Rycroft
 Rydbergs
 Rz
+Sabry
 saddlebrown
 Sadigh
 saed
@@ -2428,6 +2454,8 @@ Salles
 sandia
 Sandia
 sandybrown
+Sanitizer
+sanitizers
 sc
 scafacos
 SCAFACOS
@@ -2602,6 +2630,7 @@ Stoll
 stopstep
 Stouch
 Straatsma
+Strachan
 Stratford
 Strathclyde
 Straub
@@ -2629,6 +2658,7 @@ superset
 supersphere
 Supinski
 surfactants
+Suter
 Sutmann
 svn
 sw
@@ -2690,6 +2720,7 @@ th
 Thakkar
 thb
 thei
+Theodorou
 Theor
 thermalization
 thermalize
@@ -2812,6 +2843,7 @@ txt
 typeI
 typeJ
 typeN
+typeargs
 Tz
 Tzou
 ub
@@ -2840,6 +2872,7 @@ undump
 uniaxial
 uniaxially
 unimodal
+unitarg
 unitless
 Universite
 unix
@@ -2969,6 +3002,7 @@ Waltham
 wavepacket
 wB
 Wbody
+wca
 webpage
 Weckner
 WeinanE
diff --git a/examples/COUPLE/python/example.py b/examples/COUPLE/python/example.py
new file mode 100644
index 0000000000..ea268fe1ca
--- /dev/null
+++ b/examples/COUPLE/python/example.py
@@ -0,0 +1,36 @@
+# this example requires the LAMMPS Python package (lammps.py) to be installed
+# and LAMMPS to be loadable as shared library in LD_LIBRARY_PATH
+
+import lammps
+
+def callback(caller, ntimestep, nlocal, tag, x, fext):
+    """
+    This callback receives a caller object that was setup when registering the callback
+
+    In addition to timestep and number of local atoms, the tag and x arrays are passed as
+    NumPy arrays. The fext array is a force array allocated for fix external, which
+    can be used to apply forces to all atoms. Simply update the value in the array,
+    it will be directly written into the LAMMPS C arrays
+    """
+    print("Data passed by caller (optional)", caller)
+    print("Timestep:", ntimestep)
+    print("Number of Atoms:", nlocal)
+    print("Atom Tags:", tag)
+    print("Atom Positions:", x)
+    print("Force Additions:", fext)
+    fext.fill(1.0)
+    print("Force additions after update:", fext)
+    print("="*40)
+
+L = lammps.lammps()
+L.file("in.fix_external")
+
+# you can pass an arbitrary Python object to the callback every time it is called
+# this can be useful if you need more state information such as the LAMMPS ptr to
+# make additional library calls
+custom_object = ["Some data", L]
+
+L.set_fix_external_callback("2", callback, custom_object)
+L.command("run 100")
+
+
diff --git a/examples/COUPLE/python/in.fix_external b/examples/COUPLE/python/in.fix_external
new file mode 100644
index 0000000000..f222717c1a
--- /dev/null
+++ b/examples/COUPLE/python/in.fix_external
@@ -0,0 +1,23 @@
+# LAMMPS input for coupling LAMMPS with Python via fix external
+
+units		metal
+dimension	3
+atom_style	atomic
+atom_modify	sort 0 0.0
+
+lattice		diamond 5.43
+region		box block 0 1 0 1 0 1
+create_box	1 box
+create_atoms	1 box
+mass		1 28.08
+
+velocity	all create 300.0 87293 loop geom
+
+fix		1 all nve
+fix		2 all external pf/callback 1 1
+
+#dump		2 all image 25 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3
+
+thermo		1
diff --git a/examples/USER/eff/Be-solid/data.Be-solid b/examples/USER/eff/Be-solid/data.Be-solid
index e13aebf738..aa2e0a00aa 100644
--- a/examples/USER/eff/Be-solid/data.Be-solid
+++ b/examples/USER/eff/Be-solid/data.Be-solid
@@ -12115,7 +12115,7 @@ Atoms
 12099 2 0.000000 1 2.500000 5.740000 7.290779 1.756250
 12100 2 0.000000 -1 2.500000 5.740000 7.290779 1.756250
 12101 2 0.000000 1 2.500000 63.140000 5.965183 5.268750
-12102 2 0.000000 -1.000000 2.500000 63.140000 5.965183 5.268750
+12102 2 0.000000 -1 2.500000 63.140000 5.965183 5.268750
 12103 2 0.000000 1 2.500000 1.148000 1.988394 5.268750
 12104 2 0.000000 -1 2.500000 1.148000 1.988394 5.268750
 12105 2 0.000000 1 2.500000 3.444000 3.313991 8.781250
@@ -12123,7 +12123,7 @@ Atoms
 12107 2 0.000000 1 2.500000 5.740000 7.290779 8.781250
 12108 2 0.000000 -1 2.500000 5.740000 7.290779 8.781250
 12109 2 0.000000 1 2.500000 63.140000 5.965183 12.293750
-12110 2 0.000000 -1.000000 2.500000 63.140000 5.965183 12.293750
+12110 2 0.000000 -1 2.500000 63.140000 5.965183 12.293750
 12111 2 0.000000 1 2.500000 1.148000 1.988394 12.293750
 12112 2 0.000000 -1 2.500000 1.148000 1.988394 12.293750
 12113 2 0.000000 1 2.500000 3.444000 3.313991 15.806250
@@ -12131,7 +12131,7 @@ Atoms
 12115 2 0.000000 1 2.500000 5.740000 7.290779 15.806250
 12116 2 0.000000 -1 2.500000 5.740000 7.290779 15.806250
 12117 2 0.000000 1 2.500000 63.140000 5.965183 19.318750
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 20155 2 0.000000 1 2.500000 1.148000 62.965820 57.956250
 20156 2 0.000000 -1 2.500000 1.148000 62.965820 57.956250
 20157 2 0.000000 1 2.500000 58.548000 61.640224 61.468750
-20158 2 0.000000 -1.000000 2.500000 58.548000 61.640224 61.468750
+20158 2 0.000000 -1 2.500000 58.548000 61.640224 61.468750
 20159 2 0.000000 1 2.500000 60.844000 57.663435 61.468750
 20160 2 0.000000 -1 2.500000 60.844000 57.663435 61.468750
diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized
similarity index 88%
rename from examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
rename to examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized
index 73cb2eb270..b152dec00a 100644
--- a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
+++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized
@@ -38,6 +38,8 @@ fix myrxns all bond/react stabilization yes statted_grp .03 &
 
 fix 1 statted_grp_REACT nvt temp 300 300 100
 
+# optionally, you can customize behavior of reacting atoms,
+# by using the internally-created 'bond_react_MASTER_group', like so:
 fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
 
 thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized
new file mode 100644
index 0000000000..1e5a493821
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized
@@ -0,0 +1,48 @@
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_nylon.data
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+molecule mol2 rxn1_stp1_reacted.data_template
+molecule mol3 rxn1_stp2_unreacted.data_template
+molecule mol4 rxn1_stp2_reacted.data_template
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix myrxns all bond/react stabilization no &
+  react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
+  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+
+fix 1 all nve/limit .03
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run 1000
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
deleted file mode 100644
index 344439f94c..0000000000
--- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
+++ /dev/null
@@ -1,370 +0,0 @@
-LAMMPS (20 Apr 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
-  using 1 OpenMP thread(s) per MPI task
-# two monomer nylon example
-# reaction produces a condensed water molecule
-
-units real
-
-boundary p p p
-
-atom_style full
-
-kspace_style pppm 1.0e-4
-
-pair_style lj/class2/coul/long 8.5
-
-angle_style class2
-
-bond_style class2
-
-dihedral_style class2
-
-improper_style class2
-
-read_data tiny_nylon.data
-  orthogonal box = (-25 -25 -25) to (25 25 25)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  44 atoms
-  reading velocities ...
-  44 velocities
-  scanning bonds ...
-  9 = max bonds/atom
-  scanning angles ...
-  21 = max angles/atom
-  scanning dihedrals ...
-  29 = max dihedrals/atom
-  scanning impropers ...
-  29 = max impropers/atom
-  reading bonds ...
-  42 bonds
-  reading angles ...
-  74 angles
-  reading dihedrals ...
-  100 dihedrals
-  reading impropers ...
-  44 impropers
-  4 = max # of 1-2 neighbors
-  6 = max # of 1-3 neighbors
-  12 = max # of 1-4 neighbors
-  41 = max # of special neighbors
-
-velocity all create 300.0 4928459 dist gaussian
-
-molecule mol1 rxn1_stp1_unreacted.data_template
-Read molecule mol1:
-  18 atoms with max type 8
-  16 bonds with max type 14
-  25 angles with max type 28
-  23 dihedrals with max type 36
-  14 impropers with max type 11
-molecule mol2 rxn1_stp1_reacted.data_template
-Read molecule mol2:
-  18 atoms with max type 9
-  17 bonds with max type 13
-  31 angles with max type 27
-  39 dihedrals with max type 33
-  20 impropers with max type 1
-molecule mol3 rxn1_stp2_unreacted.data_template
-Read molecule mol3:
-  15 atoms with max type 9
-  14 bonds with max type 13
-  25 angles with max type 27
-  30 dihedrals with max type 33
-  16 impropers with max type 1
-molecule mol4 rxn1_stp2_reacted.data_template
-Read molecule mol4:
-  15 atoms with max type 11
-  13 bonds with max type 15
-  19 angles with max type 29
-  16 dihedrals with max type 32
-  10 impropers with max type 13
-
-thermo 50
-
-# dump 1 all xyz 1 test_vis.xyz
-
-fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
-WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
-WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
-dynamic group bond_react_MASTER_group defined
-dynamic group statted_grp defined
-dynamic group bond_react_MASTER_group defined
-dynamic group statted_grp defined
-
-fix 1 statted_grp nvt temp 300 300 100
-
-fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
-
-thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
-
-# restart 100 restart1 restart2
-
-run 10000
-PPPM initialization ...
-  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.0534597
-  grid = 2 2 2
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0402256
-  estimated relative force accuracy = 0.000121138
-  using double precision FFTs
-  3d grid and FFT values/proc = 343 8
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 10.5
-  ghost atom cutoff = 10.5
-  binsize = 5.25, bins = 10 10 10
-  2 neighbor lists, perpetual/occasional/extra = 1 1 0
-  (1) pair lj/class2/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-  (2) fix bond/react, occasional, copy from (1)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-WARNING: Inconsistent image flags (../domain.cpp:786)
-Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes
-Step Temp Press Density f_myrxns[1] f_myrxns[2] 
-       0          300    346.78165 0.0034851739            0            0 
-      50    296.70408    -51.30066 0.0034851739            1            0 
-     100    274.25324    46.715512 0.0034851739            1            1 
-     150    471.61579    31.321598 0.0034851739            1            1 
-     200    362.87766    42.061118 0.0034851739            1            1 
-     250    367.58058    65.303109 0.0034851739            1            1 
-     300    372.38236   -52.421725 0.0034851739            1            1 
-     350    297.69957    17.869945 0.0034851739            1            1 
-     400    258.30433     49.19156 0.0034851739            1            1 
-     450    253.34384   -5.8162637 0.0034851739            1            1 
-     500    269.96465   -43.337517 0.0034851739            1            1 
-     550    303.23718    10.180246 0.0034851739            1            1 
-     600    329.59579    -48.97461 0.0034851739            1            1 
-     650    350.42568    50.983183 0.0034851739            1            1 
-     700    342.03272     35.43465 0.0034851739            1            1 
-     750    269.23405   -41.873166 0.0034851739            1            1 
-     800    245.15025    13.953092 0.0034851739            1            1 
-     850    257.85421   -3.1492141 0.0034851739            1            1 
-     900    316.15644    7.7798301 0.0034851739            1            1 
-     950     299.9124    -15.77014 0.0034851739            1            1 
-    1000    302.89968   -17.049693 0.0034851739            1            1 
-    1050    308.91651     71.84632 0.0034851739            1            1 
-    1100    348.43932   -18.742012 0.0034851739            1            1 
-    1150    309.03036    50.536311 0.0034851739            1            1 
-    1200     318.9761   -16.905746 0.0034851739            1            1 
-    1250    320.42806 -0.057975092 0.0034851739            1            1 
-    1300     289.7824    18.200772 0.0034851739            1            1 
-    1350    284.79836   -9.1978427 0.0034851739            1            1 
-    1400    325.43292    42.082833 0.0034851739            1            1 
-    1450     261.5041   -37.823325 0.0034851739            1            1 
-    1500    298.88723   -5.1647385 0.0034851739            1            1 
-    1550    291.37403   -7.7764201 0.0034851739            1            1 
-    1600    293.83475      22.2458 0.0034851739            1            1 
-    1650    293.80611    24.202512 0.0034851739            1            1 
-    1700    291.70205   -23.397884 0.0034851739            1            1 
-    1750    292.32437   -10.671214 0.0034851739            1            1 
-    1800    302.01367   -11.671025 0.0034851739            1            1 
-    1850     322.1651    24.438331 0.0034851739            1            1 
-    1900    310.45076    45.343592 0.0034851739            1            1 
-    1950    325.91745   -19.847809 0.0034851739            1            1 
-    2000    276.89662    63.387098 0.0034851739            1            1 
-    2050    311.33783   -24.683247 0.0034851739            1            1 
-    2100     346.2336   -27.526891 0.0034851739            1            1 
-    2150    345.30604   -15.722411 0.0034851739            1            1 
-    2200     346.7718   -17.857633 0.0034851739            1            1 
-    2250    304.28676   -1.9965581 0.0034851739            1            1 
-    2300    322.56372   -31.786868 0.0034851739            1            1 
-    2350    282.64326    6.1982735 0.0034851739            1            1 
-    2400    286.65759   -63.207781 0.0034851739            1            1 
-    2450    257.05528    32.931491 0.0034851739            1            1 
-    2500    283.64386    26.912373 0.0034851739            1            1 
-    2550    299.54005    27.277039 0.0034851739            1            1 
-    2600    283.92503    14.660972 0.0034851739            1            1 
-    2650    321.93453   -18.977358 0.0034851739            1            1 
-    2700     376.7189    31.826935 0.0034851739            1            1 
-    2750    372.20075   -32.821697 0.0034851739            1            1 
-    2800    361.40604    83.035183 0.0034851739            1            1 
-    2850    332.27269   -23.927452 0.0034851739            1            1 
-    2900    331.14638  -0.12328446 0.0034851739            1            1 
-    2950    303.67489   -24.078857 0.0034851739            1            1 
-    3000    311.40462    21.563537 0.0034851739            1            1 
-    3050    284.72849   -23.849667 0.0034851739            1            1 
-    3100    303.48477    39.347763 0.0034851739            1            1 
-    3150     264.2739  -0.22299879 0.0034851739            1            1 
-    3200    300.03351    31.545323 0.0034851739            1            1 
-    3250    288.56663    5.7225228 0.0034851739            1            1 
-    3300    200.13238   -31.239655 0.0034851739            1            1 
-    3350    231.32512    16.631728 0.0034851739            1            1 
-    3400    260.57402    2.1717992 0.0034851739            1            1 
-    3450    301.47128   -42.210623 0.0034851739            1            1 
-    3500    321.77414    40.074365 0.0034851739            1            1 
-    3550    353.21858    28.387783 0.0034851739            1            1 
-    3600    331.45989   -57.800858 0.0034851739            1            1 
-    3650    303.88123     44.86596 0.0034851739            1            1 
-    3700    329.73833  -0.80615652 0.0034851739            1            1 
-    3750    297.55588  -0.49626039 0.0034851739            1            1 
-    3800    286.38794   -10.010003 0.0034851739            1            1 
-    3850    290.17417    -43.51187 0.0034851739            1            1 
-    3900    247.88933     51.23735 0.0034851739            1            1 
-    3950    332.31324   -18.194985 0.0034851739            1            1 
-    4000    325.56802    18.402825 0.0034851739            1            1 
-    4050    338.37593    36.430977 0.0034851739            1            1 
-    4100    370.95478    39.290285 0.0034851739            1            1 
-    4150    348.47859   -7.0779678 0.0034851739            1            1 
-    4200    241.30632   -33.371788 0.0034851739            1            1 
-    4250    242.17258    -9.986197 0.0034851739            1            1 
-    4300    300.85311   -7.9244294 0.0034851739            1            1 
-    4350    273.15684   -21.257283 0.0034851739            1            1 
-    4400    305.77463   -5.8720722 0.0034851739            1            1 
-    4450    314.97697      45.0373 0.0034851739            1            1 
-    4500    310.77723    16.958773 0.0034851739            1            1 
-    4550     302.1742    12.156862 0.0034851739            1            1 
-    4600    319.74799      6.84889 0.0034851739            1            1 
-    4650    270.86805   -13.767905 0.0034851739            1            1 
-    4700    249.81731   -31.197487 0.0034851739            1            1 
-    4750    285.86481   -9.8916364 0.0034851739            1            1 
-    4800    233.98321    7.1338571 0.0034851739            1            1 
-    4850    302.60551    49.262889 0.0034851739            1            1 
-    4900    316.55056    34.663247 0.0034851739            1            1 
-    4950    357.32741    11.583006 0.0034851739            1            1 
-    5000    400.21045   -8.1781061 0.0034851739            1            1 
-    5050    390.01845   -20.490275 0.0034851739            1            1 
-    5100    378.84247   -41.328757 0.0034851739            1            1 
-    5150    324.02038   -15.023862 0.0034851739            1            1 
-    5200    262.08429    10.937354 0.0034851739            1            1 
-    5250    255.75508    16.381455 0.0034851739            1            1 
-    5300    277.84989     40.68232 0.0034851739            1            1 
-    5350    302.92832    9.1989494 0.0034851739            1            1 
-    5400     283.7196   -1.6584671 0.0034851739            1            1 
-    5450    300.71266   -4.7030295 0.0034851739            1            1 
-    5500     343.5499  -0.30550044 0.0034851739            1            1 
-    5550    369.51271    21.691649 0.0034851739            1            1 
-    5600    372.69789    -38.67994 0.0034851739            1            1 
-    5650    327.41266    11.352137 0.0034851739            1            1 
-    5700    278.98614   -23.827304 0.0034851739            1            1 
-    5750    308.30054   -20.756187 0.0034851739            1            1 
-    5800    341.45594    28.058441 0.0034851739            1            1 
-    5850    322.97844   -10.731921 0.0034851739            1            1 
-    5900    304.53591    32.825279 0.0034851739            1            1 
-    5950     287.1752   -36.780091 0.0034851739            1            1 
-    6000    296.52681    18.781896 0.0034851739            1            1 
-    6050    314.25442    15.992829 0.0034851739            1            1 
-    6100    313.86576    3.4342714 0.0034851739            1            1 
-    6150    325.64196    32.392039 0.0034851739            1            1 
-    6200    367.42931   -27.160706 0.0034851739            1            1 
-    6250    369.30798    39.020934 0.0034851739            1            1 
-    6300    328.92285   -23.175157 0.0034851739            1            1 
-    6350    305.63077    4.9024453 0.0034851739            1            1 
-    6400    241.70341   -13.676629 0.0034851739            1            1 
-    6450    265.66717      2.40612 0.0034851739            1            1 
-    6500    249.36037    13.420255 0.0034851739            1            1 
-    6550    294.53814    10.853462 0.0034851739            1            1 
-    6600     308.2025    18.995308 0.0034851739            1            1 
-    6650    305.43797    -49.56785 0.0034851739            1            1 
-    6700    320.27344    11.336281 0.0034851739            1            1 
-    6750    321.78666   -23.463899 0.0034851739            1            1 
-    6800    303.40388    7.6224553 0.0034851739            1            1 
-    6850    297.18966     51.52256 0.0034851739            1            1 
-    6900    284.18909   -8.4947203 0.0034851739            1            1 
-    6950    331.03663    13.233655 0.0034851739            1            1 
-    7000    311.37928   -43.265479 0.0034851739            1            1 
-    7050    286.81661   -14.174683 0.0034851739            1            1 
-    7100    302.84119    12.048954 0.0034851739            1            1 
-    7150    297.19357   -43.111968 0.0034851739            1            1 
-    7200    332.47359    26.048249 0.0034851739            1            1 
-    7250    262.70677    41.176242 0.0034851739            1            1 
-    7300    250.61405   -23.413982 0.0034851739            1            1 
-    7350    296.91117     35.88133 0.0034851739            1            1 
-    7400    245.09229   -13.447194 0.0034851739            1            1 
-    7450    272.28131   -23.322585 0.0034851739            1            1 
-    7500    209.04985    13.871239 0.0034851739            1            1 
-    7550    255.00955    4.9325621 0.0034851739            1            1 
-    7600    312.30937   -37.368274 0.0034851739            1            1 
-    7650    305.65903    55.245496 0.0034851739            1            1 
-    7700    325.09504   -18.347711 0.0034851739            1            1 
-    7750    363.28282   -22.479686 0.0034851739            1            1 
-    7800    350.17429    26.849547 0.0034851739            1            1 
-    7850    271.70853   -17.764575 0.0034851739            1            1 
-    7900    272.66484   -11.701967 0.0034851739            1            1 
-    7950    298.60202   -12.765675 0.0034851739            1            1 
-    8000    274.58852    49.641532 0.0034851739            1            1 
-    8050    304.72347  -0.55414183 0.0034851739            1            1 
-    8100    328.30757   -39.861301 0.0034851739            1            1 
-    8150    406.67601    2.8999409 0.0034851739            1            1 
-    8200    332.20083   -51.217399 0.0034851739            1            1 
-    8250    354.50609    53.128769 0.0034851739            1            1 
-    8300     337.2758     20.68562 0.0034851739            1            1 
-    8350    361.89708   -54.185869 0.0034851739            1            1 
-    8400    305.63496    24.058529 0.0034851739            1            1 
-    8450    303.27461     4.304683 0.0034851739            1            1 
-    8500    253.53694   -10.909021 0.0034851739            1            1 
-    8550    277.03017    23.241479 0.0034851739            1            1 
-    8600    291.41844   -22.240665 0.0034851739            1            1 
-    8650    307.85368    31.919587 0.0034851739            1            1 
-    8700    309.19724   0.53529642 0.0034851739            1            1 
-    8750     354.6583    11.565515 0.0034851739            1            1 
-    8800    329.78598      19.5996 0.0034851739            1            1 
-    8850    240.79198    21.803515 0.0034851739            1            1 
-    8900    318.40749   -59.816923 0.0034851739            1            1 
-    8950    308.47211   -57.808635 0.0034851739            1            1 
-    9000    271.51207    50.943482 0.0034851739            1            1 
-    9050     249.4005    6.7529187 0.0034851739            1            1 
-    9100     221.8772    47.196092 0.0034851739            1            1 
-    9150     297.9351    4.0058184 0.0034851739            1            1 
-    9200    274.85051   -24.774393 0.0034851739            1            1 
-    9250    336.04757    5.3799028 0.0034851739            1            1 
-    9300    380.44956   -22.389381 0.0034851739            1            1 
-    9350     336.9824    23.050616 0.0034851739            1            1 
-    9400    304.46425    32.530218 0.0034851739            1            1 
-    9450    317.55591   -22.265425 0.0034851739            1            1 
-    9500    323.70901   -7.0159787 0.0034851739            1            1 
-    9550    316.07308    28.062131 0.0034851739            1            1 
-    9600    262.74608  -0.78519192 0.0034851739            1            1 
-    9650    271.55045   -21.430123 0.0034851739            1            1 
-    9700     239.6022    14.483637 0.0034851739            1            1 
-    9750     338.1437  -0.72765302 0.0034851739            1            1 
-    9800    334.50189    19.495144 0.0034851739            1            1 
-    9850    354.87554    19.272719 0.0034851739            1            1 
-    9900    334.02141   -22.393457 0.0034851739            1            1 
-    9950    293.63651    19.178873 0.0034851739            1            1 
-   10000    319.81736    21.904414 0.0034851739            1            1 
-Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms
-
-Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s
-99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.26152    | 0.26152    | 0.26152    |   0.0 | 14.14
-Bond    | 0.74069    | 0.74069    | 0.74069    |   0.0 | 40.04
-Kspace  | 0.30505    | 0.30505    | 0.30505    |   0.0 | 16.49
-Neigh   | 0.39991    | 0.39991    | 0.39991    |   0.0 | 21.62
-Comm    | 0.02261    | 0.02261    | 0.02261    |   0.0 |  1.22
-Output  | 0.0034585  | 0.0034585  | 0.0034585  |   0.0 |  0.19
-Modify  | 0.099979   | 0.099979   | 0.099979   |   0.0 |  5.40
-Other   |            | 0.01666    |            |       |  0.90
-
-Nlocal:    44 ave 44 max 44 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    44 ave 44 max 44 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    823 ave 823 max 823 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 823
-Ave neighs/atom = 18.7045
-Ave special neighs/atom = 9.77273
-Neighbor list builds = 10000
-Dangerous builds = 0
-
-# write_restart restart_longrun
-# write_data restart_longrun.data
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:01
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
deleted file mode 100644
index 377781f48f..0000000000
--- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
+++ /dev/null
@@ -1,370 +0,0 @@
-LAMMPS (20 Apr 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
-  using 1 OpenMP thread(s) per MPI task
-# two monomer nylon example
-# reaction produces a condensed water molecule
-
-units real
-
-boundary p p p
-
-atom_style full
-
-kspace_style pppm 1.0e-4
-
-pair_style lj/class2/coul/long 8.5
-
-angle_style class2
-
-bond_style class2
-
-dihedral_style class2
-
-improper_style class2
-
-read_data tiny_nylon.data
-  orthogonal box = (-25 -25 -25) to (25 25 25)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  44 atoms
-  reading velocities ...
-  44 velocities
-  scanning bonds ...
-  9 = max bonds/atom
-  scanning angles ...
-  21 = max angles/atom
-  scanning dihedrals ...
-  29 = max dihedrals/atom
-  scanning impropers ...
-  29 = max impropers/atom
-  reading bonds ...
-  42 bonds
-  reading angles ...
-  74 angles
-  reading dihedrals ...
-  100 dihedrals
-  reading impropers ...
-  44 impropers
-  4 = max # of 1-2 neighbors
-  6 = max # of 1-3 neighbors
-  12 = max # of 1-4 neighbors
-  41 = max # of special neighbors
-
-velocity all create 300.0 4928459 dist gaussian
-
-molecule mol1 rxn1_stp1_unreacted.data_template
-Read molecule mol1:
-  18 atoms with max type 8
-  16 bonds with max type 14
-  25 angles with max type 28
-  23 dihedrals with max type 36
-  14 impropers with max type 11
-molecule mol2 rxn1_stp1_reacted.data_template
-Read molecule mol2:
-  18 atoms with max type 9
-  17 bonds with max type 13
-  31 angles with max type 27
-  39 dihedrals with max type 33
-  20 impropers with max type 1
-molecule mol3 rxn1_stp2_unreacted.data_template
-Read molecule mol3:
-  15 atoms with max type 9
-  14 bonds with max type 13
-  25 angles with max type 27
-  30 dihedrals with max type 33
-  16 impropers with max type 1
-molecule mol4 rxn1_stp2_reacted.data_template
-Read molecule mol4:
-  15 atoms with max type 11
-  13 bonds with max type 15
-  19 angles with max type 29
-  16 dihedrals with max type 32
-  10 impropers with max type 13
-
-thermo 50
-
-# dump 1 all xyz 1 test_vis.xyz
-
-fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
-WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
-WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
-dynamic group bond_react_MASTER_group defined
-dynamic group statted_grp defined
-dynamic group bond_react_MASTER_group defined
-dynamic group statted_grp defined
-
-fix 1 statted_grp nvt temp 300 300 100
-
-fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
-
-thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
-
-# restart 100 restart1 restart2
-
-run 10000
-PPPM initialization ...
-  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.0534597
-  grid = 2 2 2
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0402256
-  estimated relative force accuracy = 0.000121138
-  using double precision FFTs
-  3d grid and FFT values/proc = 252 2
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 10.5
-  ghost atom cutoff = 10.5
-  binsize = 5.25, bins = 10 10 10
-  2 neighbor lists, perpetual/occasional/extra = 1 1 0
-  (1) pair lj/class2/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-  (2) fix bond/react, occasional, copy from (1)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-WARNING: Inconsistent image flags (../domain.cpp:786)
-Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
-Step Temp Press Density f_myrxns[1] f_myrxns[2] 
-       0          300    346.78165 0.0034851739            0            0 
-      50    296.70408    -51.30066 0.0034851739            1            0 
-     100    274.25324    46.715512 0.0034851739            1            1 
-     150    471.61579    31.321598 0.0034851739            1            1 
-     200    362.87766    42.061118 0.0034851739            1            1 
-     250    367.58058    65.303109 0.0034851739            1            1 
-     300    372.38236   -52.421725 0.0034851739            1            1 
-     350    297.69957    17.869945 0.0034851739            1            1 
-     400    258.30433     49.19156 0.0034851739            1            1 
-     450    253.34384   -5.8162637 0.0034851739            1            1 
-     500    269.96465   -43.337517 0.0034851739            1            1 
-     550    303.23718    10.180246 0.0034851739            1            1 
-     600    329.59579    -48.97461 0.0034851739            1            1 
-     650    350.42568    50.983183 0.0034851739            1            1 
-     700    342.03272     35.43465 0.0034851739            1            1 
-     750    269.23405   -41.873166 0.0034851739            1            1 
-     800    245.15025    13.953092 0.0034851739            1            1 
-     850    257.85421   -3.1492141 0.0034851739            1            1 
-     900    316.15644    7.7798301 0.0034851739            1            1 
-     950     299.9124    -15.77014 0.0034851739            1            1 
-    1000    302.89968   -17.049693 0.0034851739            1            1 
-    1050    308.91651     71.84632 0.0034851739            1            1 
-    1100    348.43932   -18.742012 0.0034851739            1            1 
-    1150    309.03036    50.536311 0.0034851739            1            1 
-    1200     318.9761   -16.905746 0.0034851739            1            1 
-    1250    320.42806 -0.057975092 0.0034851739            1            1 
-    1300     289.7824    18.200772 0.0034851739            1            1 
-    1350    284.79836   -9.1978427 0.0034851739            1            1 
-    1400    325.43292    42.082833 0.0034851739            1            1 
-    1450     261.5041   -37.823325 0.0034851739            1            1 
-    1500    298.88723   -5.1647385 0.0034851739            1            1 
-    1550    291.37403   -7.7764201 0.0034851739            1            1 
-    1600    293.83475      22.2458 0.0034851739            1            1 
-    1650    293.80611    24.202512 0.0034851739            1            1 
-    1700    291.70205   -23.397884 0.0034851739            1            1 
-    1750    292.32437   -10.671214 0.0034851739            1            1 
-    1800    302.01367   -11.671025 0.0034851739            1            1 
-    1850     322.1651    24.438331 0.0034851739            1            1 
-    1900    310.45076    45.343592 0.0034851739            1            1 
-    1950    325.91745   -19.847809 0.0034851739            1            1 
-    2000    276.89662    63.387098 0.0034851739            1            1 
-    2050    311.33783   -24.683247 0.0034851739            1            1 
-    2100     346.2336   -27.526891 0.0034851739            1            1 
-    2150    345.30604   -15.722411 0.0034851739            1            1 
-    2200     346.7718   -17.857633 0.0034851739            1            1 
-    2250    304.28676   -1.9965581 0.0034851739            1            1 
-    2300    322.56372   -31.786868 0.0034851739            1            1 
-    2350    282.64326    6.1982735 0.0034851739            1            1 
-    2400    286.65759   -63.207781 0.0034851739            1            1 
-    2450    257.05528    32.931491 0.0034851739            1            1 
-    2500    283.64386    26.912373 0.0034851739            1            1 
-    2550    299.54005    27.277039 0.0034851739            1            1 
-    2600    283.92503    14.660972 0.0034851739            1            1 
-    2650    321.93453   -18.977358 0.0034851739            1            1 
-    2700     376.7189    31.826935 0.0034851739            1            1 
-    2750    372.20075   -32.821697 0.0034851739            1            1 
-    2800    361.40604    83.035183 0.0034851739            1            1 
-    2850    332.27269   -23.927452 0.0034851739            1            1 
-    2900    331.14638  -0.12328446 0.0034851739            1            1 
-    2950    303.67489   -24.078857 0.0034851739            1            1 
-    3000    311.40462    21.563537 0.0034851739            1            1 
-    3050    284.72849   -23.849667 0.0034851739            1            1 
-    3100    303.48477    39.347763 0.0034851739            1            1 
-    3150     264.2739  -0.22299878 0.0034851739            1            1 
-    3200    300.03351    31.545323 0.0034851739            1            1 
-    3250    288.56663    5.7225229 0.0034851739            1            1 
-    3300    200.13238   -31.239655 0.0034851739            1            1 
-    3350    231.32512    16.631728 0.0034851739            1            1 
-    3400    260.57402    2.1717992 0.0034851739            1            1 
-    3450    301.47128   -42.210623 0.0034851739            1            1 
-    3500    321.77414    40.074365 0.0034851739            1            1 
-    3550    353.21858    28.387783 0.0034851739            1            1 
-    3600    331.45989   -57.800858 0.0034851739            1            1 
-    3650    303.88123     44.86596 0.0034851739            1            1 
-    3700    329.73833   -0.8061567 0.0034851739            1            1 
-    3750    297.55588  -0.49626022 0.0034851739            1            1 
-    3800    286.38794   -10.010003 0.0034851739            1            1 
-    3850    290.17417    -43.51187 0.0034851739            1            1 
-    3900    247.88933     51.23735 0.0034851739            1            1 
-    3950    332.31324   -18.194985 0.0034851739            1            1 
-    4000    325.56802    18.402825 0.0034851739            1            1 
-    4050    338.37594    36.430977 0.0034851739            1            1 
-    4100    370.95478    39.290285 0.0034851739            1            1 
-    4150    348.47859   -7.0779683 0.0034851739            1            1 
-    4200    241.30632   -33.371789 0.0034851739            1            1 
-    4250    242.17258   -9.9861962 0.0034851739            1            1 
-    4300    300.85311    -7.924429 0.0034851739            1            1 
-    4350    273.15684   -21.257282 0.0034851739            1            1 
-    4400    305.77464   -5.8720712 0.0034851739            1            1 
-    4450    314.97697    45.037299 0.0034851739            1            1 
-    4500    310.77723    16.958771 0.0034851739            1            1 
-    4550    302.17421    12.156862 0.0034851739            1            1 
-    4600    319.74799    6.8488914 0.0034851739            1            1 
-    4650    270.86805   -13.767907 0.0034851739            1            1 
-    4700    249.81731   -31.197484 0.0034851739            1            1 
-    4750    285.86481   -9.8916332 0.0034851739            1            1 
-    4800    233.98321    7.1338518 0.0034851739            1            1 
-    4850    302.60551    49.262886 0.0034851739            1            1 
-    4900    316.55055    34.663238 0.0034851739            1            1 
-    4950    357.32741    11.583013 0.0034851739            1            1 
-    5000    400.21044   -8.1780861 0.0034851739            1            1 
-    5050    390.01845   -20.490268 0.0034851739            1            1 
-    5100    378.84249   -41.328772 0.0034851739            1            1 
-    5150    324.02039   -15.023852 0.0034851739            1            1 
-    5200    262.08427    10.937367 0.0034851739            1            1 
-    5250    255.75506    16.381495 0.0034851739            1            1 
-    5300    277.84991    40.682283 0.0034851739            1            1 
-    5350    302.92834    9.1989644 0.0034851739            1            1 
-    5400    283.71964   -1.6583895 0.0034851739            1            1 
-    5450    300.71261    -4.703054 0.0034851739            1            1 
-    5500    343.54987  -0.30546396 0.0034851739            1            1 
-    5550    369.51272    21.691639 0.0034851739            1            1 
-    5600    372.69786   -38.679919 0.0034851739            1            1 
-    5650    327.41256    11.352201 0.0034851739            1            1 
-    5700     278.9861    -23.82728 0.0034851739            1            1 
-    5750    308.30037   -20.756238 0.0034851739            1            1 
-    5800     341.4559    28.058314 0.0034851739            1            1 
-    5850     322.9786   -10.731862 0.0034851739            1            1 
-    5900    304.53598    32.825105 0.0034851739            1            1 
-    5950    287.17515   -36.780057 0.0034851739            1            1 
-    6000    296.52688    18.782156 0.0034851739            1            1 
-    6050    314.25411     15.99272 0.0034851739            1            1 
-    6100    313.86572    3.4344108 0.0034851739            1            1 
-    6150    325.64197     32.39212 0.0034851739            1            1 
-    6200     367.4298   -27.161154 0.0034851739            1            1 
-    6250    369.30937    39.020881 0.0034851739            1            1 
-    6300    328.92245   -23.175612 0.0034851739            1            1 
-    6350     305.6293    4.9011587 0.0034851739            1            1 
-    6400    241.70456   -13.675247 0.0034851739            1            1 
-    6450    265.66574    2.4049735 0.0034851739            1            1 
-    6500     249.3592    13.420453 0.0034851739            1            1 
-    6550     294.5367    10.856753 0.0034851739            1            1 
-    6600    308.20246    18.992923 0.0034851739            1            1 
-    6650    305.43756    -49.57151 0.0034851739            1            1 
-    6700    320.27395    11.339101 0.0034851739            1            1 
-    6750     321.7875   -23.463361 0.0034851739            1            1 
-    6800    303.40316    7.6256997 0.0034851739            1            1 
-    6850    297.18652     51.52186 0.0034851739            1            1 
-    6900    284.19084    -8.496294 0.0034851739            1            1 
-    6950    331.04173    13.227745 0.0034851739            1            1 
-    7000    311.38027    -43.26105 0.0034851739            1            1 
-    7050    286.82046   -14.171194 0.0034851739            1            1 
-    7100    302.81691    12.058085 0.0034851739            1            1 
-    7150    297.18018   -43.110658 0.0034851739            1            1 
-    7200    332.46131    26.051496 0.0034851739            1            1 
-    7250    262.72288    41.161451 0.0034851739            1            1 
-    7300    250.62739   -23.440907 0.0034851739            1            1 
-    7350    296.92141    35.869216 0.0034851739            1            1 
-    7400    245.06807   -13.467896 0.0034851739            1            1 
-    7450     272.2659   -23.292836 0.0034851739            1            1 
-    7500    209.05776    13.888665 0.0034851739            1            1 
-    7550    255.03716    4.9662624 0.0034851739            1            1 
-    7600    312.26011   -37.350427 0.0034851739            1            1 
-    7650     305.5823    55.208039 0.0034851739            1            1 
-    7700    325.13382   -18.370791 0.0034851739            1            1 
-    7750    363.24898   -22.473126 0.0034851739            1            1 
-    7800    350.19254    26.792307 0.0034851739            1            1 
-    7850    271.76418   -17.843445 0.0034851739            1            1 
-    7900    272.70301   -11.709349 0.0034851739            1            1 
-    7950     298.5993   -12.736235 0.0034851739            1            1 
-    8000    274.52611    49.657345 0.0034851739            1            1 
-    8050    304.73711  -0.52485689 0.0034851739            1            1 
-    8100    328.29239   -39.901891 0.0034851739            1            1 
-    8150    406.52096    2.8669076 0.0034851739            1            1 
-    8200    332.17309   -51.168754 0.0034851739            1            1 
-    8250    354.68419    53.003157 0.0034851739            1            1 
-    8300    337.28934    20.766408 0.0034851739            1            1 
-    8350    361.81133   -54.159227 0.0034851739            1            1 
-    8400    305.59597    24.011667 0.0034851739            1            1 
-    8450    303.25823     4.423341 0.0034851739            1            1 
-    8500    253.50747   -11.026949 0.0034851739            1            1 
-    8550    277.13504    23.204625 0.0034851739            1            1 
-    8600    291.40211   -22.253861 0.0034851739            1            1 
-    8650    307.93765     32.14162 0.0034851739            1            1 
-    8700     309.1529   0.36279434 0.0034851739            1            1 
-    8750    355.10326    11.677219 0.0034851739            1            1 
-    8800    330.21328    19.235269 0.0034851739            1            1 
-    8850    241.29109    21.707386 0.0034851739            1            1 
-    8900    319.15363   -60.010115 0.0034851739            1            1 
-    8950    308.88552   -57.637014 0.0034851739            1            1 
-    9000    272.22373     51.15837 0.0034851739            1            1 
-    9050    248.84947    7.3390565 0.0034851739            1            1 
-    9100    221.91564    48.387079 0.0034851739            1            1 
-    9150    298.03506    2.9058639 0.0034851739            1            1 
-    9200    274.25114   -24.597819 0.0034851739            1            1 
-    9250    334.08373    5.1079577 0.0034851739            1            1 
-    9300    383.07285   -23.274763 0.0034851739            1            1 
-    9350    335.00581     20.94212 0.0034851739            1            1 
-    9400    309.23862    34.074744 0.0034851739            1            1 
-    9450    312.62262   -28.468057 0.0034851739            1            1 
-    9500    324.54274     2.851136 0.0034851739            1            1 
-    9550    313.32781    22.468182 0.0034851739            1            1 
-    9600    269.04372     4.064934 0.0034851739            1            1 
-    9650    270.98476   -21.520127 0.0034851739            1            1 
-    9700     236.8736    16.250728 0.0034851739            1            1 
-    9750    333.94686    1.6864148 0.0034851739            1            1 
-    9800    330.91875    12.150018 0.0034851739            1            1 
-    9850     343.8603    25.338853 0.0034851739            1            1 
-    9900    330.93364   -28.292992 0.0034851739            1            1 
-    9950    291.25518    25.795948 0.0034851739            1            1 
-   10000    319.25565    25.323846 0.0034851739            1            1 
-Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms
-
-Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s
-93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0030422  | 0.10454    | 0.35211    |  44.8 |  2.94
-Bond    | 0.0063896  | 0.29222    | 0.94356    |  71.3 |  8.22
-Kspace  | 0.88508    | 1.6486     | 1.979      |  35.1 | 46.39
-Neigh   | 0.61154    | 0.62212    | 0.63307    |   1.0 | 17.51
-Comm    | 0.18944    | 0.24549    | 0.29196    |   7.9 |  6.91
-Output  | 0.0050066  | 0.011804   | 0.032134   |  10.8 |  0.33
-Modify  | 0.52282    | 0.60522    | 0.69588    |   7.9 | 17.03
-Other   |            | 0.02359    |            |       |  0.66
-
-Nlocal:    11 ave 44 max 0 min
-Histogram: 3 0 0 0 0 0 0 0 0 1
-Nghost:    33 ave 44 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 3
-Neighs:    205.75 ave 823 max 0 min
-Histogram: 3 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 823
-Ave neighs/atom = 18.7045
-Ave special neighs/atom = 9.77273
-Neighbor list builds = 10000
-Dangerous builds = 0
-
-# write_restart restart_longrun
-# write_data restart_longrun.data
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1
new file mode 100644
index 0000000000..de1167c652
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1
@@ -0,0 +1,148 @@
+LAMMPS (5 Jun 2019)
+Reading data file ...
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  44 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000181113 secs
+  read_data CPU = 0.0251833 secs
+Read molecule mol1:
+  18 atoms with max type 8
+  16 bonds with max type 14
+  25 angles with max type 28
+  23 dihedrals with max type 36
+  14 impropers with max type 11
+Read molecule mol2:
+  18 atoms with max type 9
+  17 bonds with max type 13
+  31 angles with max type 27
+  39 dihedrals with max type 33
+  20 impropers with max type 1
+Read molecule mol3:
+  15 atoms with max type 9
+  14 bonds with max type 13
+  25 angles with max type 27
+  30 dihedrals with max type 33
+  16 impropers with max type 1
+Read molecule mol4:
+  15 atoms with max type 11
+  13 bonds with max type 15
+  19 angles with max type 29
+  16 dihedrals with max type 32
+  10 impropers with max type 13
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:319)
+  G vector (1/distance) = 0.0534597
+  grid = 2 2 2
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0402256
+  estimated relative force accuracy = 0.000121138
+  using double precision FFTs
+  3d grid and FFT values/proc = 343 8
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+WARNING: Inconsistent image flags (../domain.cpp:784)
+Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0 
+      50    293.70542   -52.547388 0.0034851739            1            0 
+     100    276.36755     54.81826 0.0034851739            1            1 
+     150    448.65869    16.874435 0.0034851739            1            1 
+     200    379.84257    11.578545 0.0034851739            1            1 
+     250    298.21983    90.656585 0.0034851739            1            1 
+     300     333.3111   -30.139607 0.0034851739            1            1 
+     350    266.57108    6.4505134 0.0034851739            1            1 
+     400    264.05476    10.513204 0.0034851739            1            1 
+     450    250.70418   -18.635379 0.0034851739            1            1 
+     500    261.21632    10.231013 0.0034851739            1            1 
+     550    309.89024   -8.8299506 0.0034851739            1            1 
+     600    373.45851    30.368993 0.0034851739            1            1 
+     650    338.26242    9.0362267 0.0034851739            1            1 
+     700    295.67794   -5.6007538 0.0034851739            1            1 
+     750    310.86563   -59.228181 0.0034851739            1            1 
+     800    286.22678   -9.9022407 0.0034851739            1            1 
+     850    218.42135    27.845352 0.0034851739            1            1 
+     900    259.62551    24.216336 0.0034851739            1            1 
+     950    250.21307   -14.560985 0.0034851739            1            1 
+    1000    274.29245  -0.38768626 0.0034851739            1            1 
+Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms
+
+Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s
+87.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.031135   | 0.031135   | 0.031135   |   0.0 |  9.13
+Bond    | 0.12623    | 0.12623    | 0.12623    |   0.0 | 37.01
+Kspace  | 0.036491   | 0.036491   | 0.036491   |   0.0 | 10.70
+Neigh   | 0.046395   | 0.046395   | 0.046395   |   0.0 | 13.60
+Comm    | 0.0025396  | 0.0025396  | 0.0025396  |   0.0 |  0.74
+Output  | 0.07775    | 0.07775    | 0.07775    |   0.0 | 22.80
+Modify  | 0.019219   | 0.019219   | 0.019219   |   0.0 |  5.64
+Other   |            | 0.001306   |            |       |  0.38
+
+Nlocal:    44 ave 44 max 44 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2 ave 2 max 2 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    740 ave 740 max 740 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 740
+Ave neighs/atom = 16.8182
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4
new file mode 100644
index 0000000000..b9c7a3ba15
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4
@@ -0,0 +1,148 @@
+LAMMPS (5 Jun 2019)
+Reading data file ...
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  44 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000178751 secs
+  read_data CPU = 0.0385782 secs
+Read molecule mol1:
+  18 atoms with max type 8
+  16 bonds with max type 14
+  25 angles with max type 28
+  23 dihedrals with max type 36
+  14 impropers with max type 11
+Read molecule mol2:
+  18 atoms with max type 9
+  17 bonds with max type 13
+  31 angles with max type 27
+  39 dihedrals with max type 33
+  20 impropers with max type 1
+Read molecule mol3:
+  15 atoms with max type 9
+  14 bonds with max type 13
+  25 angles with max type 27
+  30 dihedrals with max type 33
+  16 impropers with max type 1
+Read molecule mol4:
+  15 atoms with max type 11
+  13 bonds with max type 15
+  19 angles with max type 29
+  16 dihedrals with max type 32
+  10 impropers with max type 13
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:319)
+  G vector (1/distance) = 0.0534597
+  grid = 2 2 2
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0402256
+  estimated relative force accuracy = 0.000121138
+  using double precision FFTs
+  3d grid and FFT values/proc = 252 2
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+WARNING: Inconsistent image flags (../domain.cpp:784)
+Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0 
+      50    293.70542   -52.547388 0.0034851739            1            0 
+     100    276.36755     54.81826 0.0034851739            1            1 
+     150    448.65869    16.874435 0.0034851739            1            1 
+     200    379.84257    11.578545 0.0034851739            1            1 
+     250    298.21983    90.656585 0.0034851739            1            1 
+     300     333.3111   -30.139607 0.0034851739            1            1 
+     350    266.57108    6.4505134 0.0034851739            1            1 
+     400    264.05476    10.513204 0.0034851739            1            1 
+     450    250.70418   -18.635379 0.0034851739            1            1 
+     500    261.21632    10.231013 0.0034851739            1            1 
+     550    309.89024   -8.8299506 0.0034851739            1            1 
+     600    373.45851    30.368993 0.0034851739            1            1 
+     650    338.26242    9.0362267 0.0034851739            1            1 
+     700    295.67794   -5.6007538 0.0034851739            1            1 
+     750    310.86563   -59.228181 0.0034851739            1            1 
+     800    286.22678   -9.9022407 0.0034851739            1            1 
+     850    218.42135    27.845352 0.0034851739            1            1 
+     900    259.62551    24.216336 0.0034851739            1            1 
+     950    250.21307   -14.560985 0.0034851739            1            1 
+    1000    274.29245  -0.38768626 0.0034851739            1            1 
+Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms
+
+Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s
+98.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00023773 | 0.0077322  | 0.016042   |   8.4 |  2.85
+Bond    | 0.00073385 | 0.032108   | 0.08446    |  19.4 | 11.84
+Kspace  | 0.041659   | 0.098095   | 0.13373    |  12.3 | 36.16
+Neigh   | 0.028894   | 0.029247   | 0.029558   |   0.1 | 10.78
+Comm    | 0.012367   | 0.013642   | 0.01503    |   0.9 |  5.03
+Output  | 0.032475   | 0.040504   | 0.061019   |   5.9 | 14.93
+Modify  | 0.032934   | 0.049086   | 0.0577     |   4.3 | 18.10
+Other   |            | 0.0008281  |            |       |  0.31
+
+Nlocal:    11 ave 21 max 0 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost:    32.5 ave 43 max 23 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    185 ave 376 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 740
+Ave neighs/atom = 16.8182
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1
new file mode 100644
index 0000000000..14cac1dfad
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1
@@ -0,0 +1,147 @@
+LAMMPS (5 Jun 2019)
+Reading data file ...
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  44 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000217102 secs
+  read_data CPU = 0.00630778 secs
+Read molecule mol1:
+  18 atoms with max type 8
+  16 bonds with max type 14
+  25 angles with max type 28
+  23 dihedrals with max type 36
+  14 impropers with max type 11
+Read molecule mol2:
+  18 atoms with max type 9
+  17 bonds with max type 13
+  31 angles with max type 27
+  39 dihedrals with max type 33
+  20 impropers with max type 1
+Read molecule mol3:
+  15 atoms with max type 9
+  14 bonds with max type 13
+  25 angles with max type 27
+  30 dihedrals with max type 33
+  16 impropers with max type 1
+Read molecule mol4:
+  15 atoms with max type 11
+  13 bonds with max type 15
+  19 angles with max type 29
+  16 dihedrals with max type 32
+  10 impropers with max type 13
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
+dynamic group bond_react_MASTER_group defined
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:319)
+  G vector (1/distance) = 0.0534597
+  grid = 2 2 2
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0402256
+  estimated relative force accuracy = 0.000121138
+  using double precision FFTs
+  3d grid and FFT values/proc = 343 8
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+WARNING: Inconsistent image flags (../domain.cpp:784)
+Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0 
+      50    416.49412   -20.293038 0.0034851739            1            0 
+     100    746.49323    91.912227 0.0034851739            1            1 
+     150    515.15907   -1.4024709 0.0034851739            1            1 
+     200    441.14572   -19.333087 0.0034851739            1            1 
+     250    376.40996    30.717679 0.0034851739            1            1 
+     300    326.15127   -3.0433799 0.0034851739            1            1 
+     350    326.21116     6.235391 0.0034851739            1            1 
+     400    366.48556    3.9807338 0.0034851739            1            1 
+     450    313.79097    7.6674629 0.0034851739            1            1 
+     500    278.89836    14.102052 0.0034851739            1            1 
+     550    267.50214    18.241417 0.0034851739            1            1 
+     600    276.28064    7.4649611 0.0034851739            1            1 
+     650    255.26713   -8.5258573 0.0034851739            1            1 
+     700    258.59752   -5.3341215 0.0034851739            1            1 
+     750    263.71264    33.369869 0.0034851739            1            1 
+     800    246.22976   -15.349137 0.0034851739            1            1 
+     850    255.93887    16.331669 0.0034851739            1            1 
+     900    239.72525  -0.20075789 0.0034851739            1            1 
+     950    213.73064     12.17619 0.0034851739            1            1 
+    1000    218.25094   -9.0955642 0.0034851739            1            1 
+Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms
+
+Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s
+91.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.031941   | 0.031941   | 0.031941   |   0.0 |  9.17
+Bond    | 0.13031    | 0.13031    | 0.13031    |   0.0 | 37.42
+Kspace  | 0.037554   | 0.037554   | 0.037554   |   0.0 | 10.78
+Neigh   | 0.047397   | 0.047397   | 0.047397   |   0.0 | 13.61
+Comm    | 0.0025814  | 0.0025814  | 0.0025814  |   0.0 |  0.74
+Output  | 0.083526   | 0.083526   | 0.083526   |   0.0 | 23.98
+Modify  | 0.013602   | 0.013602   | 0.013602   |   0.0 |  3.91
+Other   |            | 0.001336   |            |       |  0.38
+
+Nlocal:    44 ave 44 max 44 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    3 ave 3 max 3 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    818 ave 818 max 818 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 818
+Ave neighs/atom = 18.5909
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4
new file mode 100644
index 0000000000..6b13dd60d3
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4
@@ -0,0 +1,147 @@
+LAMMPS (5 Jun 2019)
+Reading data file ...
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  44 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000163256 secs
+  read_data CPU = 0.0244579 secs
+Read molecule mol1:
+  18 atoms with max type 8
+  16 bonds with max type 14
+  25 angles with max type 28
+  23 dihedrals with max type 36
+  14 impropers with max type 11
+Read molecule mol2:
+  18 atoms with max type 9
+  17 bonds with max type 13
+  31 angles with max type 27
+  39 dihedrals with max type 33
+  20 impropers with max type 1
+Read molecule mol3:
+  15 atoms with max type 9
+  14 bonds with max type 13
+  25 angles with max type 27
+  30 dihedrals with max type 33
+  16 impropers with max type 1
+Read molecule mol4:
+  15 atoms with max type 11
+  13 bonds with max type 15
+  19 angles with max type 29
+  16 dihedrals with max type 32
+  10 impropers with max type 13
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
+dynamic group bond_react_MASTER_group defined
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:319)
+  G vector (1/distance) = 0.0534597
+  grid = 2 2 2
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0402256
+  estimated relative force accuracy = 0.000121138
+  using double precision FFTs
+  3d grid and FFT values/proc = 252 2
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+WARNING: Inconsistent image flags (../domain.cpp:784)
+Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0 
+      50    416.49412   -20.293038 0.0034851739            1            0 
+     100    746.49323    91.912227 0.0034851739            1            1 
+     150    515.15907   -1.4024709 0.0034851739            1            1 
+     200    441.14572   -19.333087 0.0034851739            1            1 
+     250    376.40996    30.717679 0.0034851739            1            1 
+     300    326.15127   -3.0433799 0.0034851739            1            1 
+     350    326.21116     6.235391 0.0034851739            1            1 
+     400    366.48556    3.9807338 0.0034851739            1            1 
+     450    313.79097    7.6674629 0.0034851739            1            1 
+     500    278.89836    14.102052 0.0034851739            1            1 
+     550    267.50214    18.241417 0.0034851739            1            1 
+     600    276.28064    7.4649611 0.0034851739            1            1 
+     650    255.26713   -8.5258573 0.0034851739            1            1 
+     700    258.59752   -5.3341215 0.0034851739            1            1 
+     750    263.71264    33.369869 0.0034851739            1            1 
+     800    246.22976   -15.349137 0.0034851739            1            1 
+     850    255.93887    16.331669 0.0034851739            1            1 
+     900    239.72525  -0.20075789 0.0034851739            1            1 
+     950    213.73064     12.17619 0.0034851739            1            1 
+    1000    218.25094   -9.0955642 0.0034851739            1            1 
+Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms
+
+Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00014252 | 0.0090715  | 0.021332   |   9.6 |  3.56
+Bond    | 0.00047028 | 0.037261   | 0.10789    |  22.7 | 14.62
+Kspace  | 0.051006   | 0.12756    | 0.1693     |  13.6 | 50.04
+Neigh   | 0.035644   | 0.036088   | 0.036523   |   0.2 | 14.16
+Comm    | 0.013984   | 0.016074   | 0.018676   |   1.6 |  6.31
+Output  | 0.0002816  | 0.00033726 | 0.00044251 |   0.0 |  0.13
+Modify  | 0.023697   | 0.027803   | 0.033552   |   2.5 | 10.91
+Other   |            | 0.0007123  |            |       |  0.28
+
+Nlocal:    11 ave 29 max 0 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+Nghost:    25 ave 31 max 12 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Neighs:    204.5 ave 443 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 818
+Ave neighs/atom = 18.5909
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/USER/misc/hma/README b/examples/USER/misc/hma/README
new file mode 100644
index 0000000000..5af6ec15fa
--- /dev/null
+++ b/examples/USER/misc/hma/README
@@ -0,0 +1,22 @@
+The example input script sets up a simple FCC crystal using the Lennard-Jones
+potential. The script sets up the HMA compute to calculate the energy, pressure
+and heat capacity.  The output columns are:
+
+1: timestep
+2: measured temperature
+3: potential energy
+4: HMA potential energy
+5: pressure
+6: HMA pressure
+7: HMA heat capacity contribution
+
+Averages of the potential energy (#3 and #4) agree although #4 (HMA) is more precise.
+
+Averages of the pressure (#5 and #6) agree once the ideal gas
+contribution is included; #6 (HMA) is more precise.
+
+The heat capacity can be computed from colume #3 (convential) as
+Cv = Var(#3)/(k T^2)
+
+With HMA, the heat capacity can be computed from column #4 and #7 as
+Cv = #7 + Var(#4)/(k T^2)
diff --git a/examples/USER/misc/hma/hma.in b/examples/USER/misc/hma/hma.in
new file mode 100644
index 0000000000..96f2ca1f2a
--- /dev/null
+++ b/examples/USER/misc/hma/hma.in
@@ -0,0 +1,36 @@
+# Harmonically mapped average example
+
+units lj 
+dimension 3 
+boundary p p p 
+atom_style atomic 
+atom_modify map array
+# ---------- Create Atoms ----------------------------
+lattice 	fcc 1.0
+region	box block 0 4 0 4 0 4 units lattice
+create_box	1 box
+lattice	fcc 1.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1  
+create_atoms 1 region box
+# ---------- Define Interatomic Potential --------------------- 
+pair_style lj/smooth/linear 3
+pair_coeff * * 1.0 1.0 
+mass 1 1.0
+
+atom_modify sort 0 1
+velocity all create 0.1 45678 dist gaussian
+
+compute u all pe 
+  
+compute p all pressure NULL pair  
+
+compute hma all hma settemp u p 9.579586686264458 cv
+
+timestep 0.005
+
+fix settemp all nvt temp 1.0 1.0 0.5
+thermo_style custom elapsed temp c_u c_hma[1] c_p c_hma[2] c_hma[3]
+thermo_modify format float '%22.15e'
+thermo 500
+run 20000
+thermo 20
+run 200000
diff --git a/examples/USER/misc/hma/log.6Nov18.hma.g++.1 b/examples/USER/misc/hma/log.6Nov18.hma.g++.1
new file mode 100644
index 0000000000..fba304d783
--- /dev/null
+++ b/examples/USER/misc/hma/log.6Nov18.hma.g++.1
@@ -0,0 +1,10159 @@
+LAMMPS (31 Aug 2018)
+# Harmonically mapped average example
+
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+atom_modify map array
+# ---------- Create Atoms ----------------------------
+lattice 	fcc 1.0
+Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
+region	box block 0 4 0 4 0 4 units lattice
+create_box	1 box
+Created orthogonal box = (0 0 0) to (6.3496 6.3496 6.3496)
+  1 by 1 by 1 MPI processor grid
+lattice	fcc 1.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
+Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
+create_atoms 1 region box
+Created 256 atoms
+  Time spent = 0.000558853 secs
+# ---------- Define Interatomic Potential ---------------------
+pair_style lj/smooth/linear 3
+pair_coeff * * 1.0 1.0
+mass 1 1.0
+
+atom_modify sort 0 1
+velocity all create 0.1 45678 dist gaussian
+
+compute u all pe
+
+compute p all pressure NULL pair
+
+compute hma all HMA settemp u p 9.579586686264458 cv
+
+timestep 0.005
+
+fix settemp all nvt temp 1.0 1.0 0.5
+thermo_style custom elapsed temp c_u c_hma[1] c_p c_hma[2] c_hma[3]
+thermo_modify format float '%22.15e'
+thermo 500
+run 20000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 4 4 4
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/smooth/linear, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute HMA, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.425 | 3.425 | 3.425 Mbytes
+Elapsed Temp c_u c_hma[1] c_p c_hma[2] c_hma[3] 
+       0  9.999999999999984e-02 -7.321210550029651e+00 -5.827069925029651e+00 -3.541123363606526e+00  6.038463322657933e+00  8.693908581888376e+03 
+     500  2.386148283497847e-01 -7.031289207724356e+00 -5.841955950103862e+00 -1.905706169928171e+00  5.923629444055504e+00  8.738341241696249e+03 
+    1000  1.033640532939756e+00 -5.899129588008281e+00 -5.989693420271868e+00  4.270084606318116e+00  4.750053066752854e+00  9.185409687897396e+03 
+    1500  9.066678783388608e-01 -6.084949363864708e+00 -6.008077972326689e+00  3.223989663631114e+00  4.665397089651815e+00  9.241882696308397e+03 
+    2000  8.653666754537616e-01 -6.040261189331211e+00 -6.030563879284796e+00  3.468617809376976e+00  4.524301264317375e+00  9.311127705836057e+03 
+    2500  1.037531298248839e+00 -6.132639377068311e+00 -5.988640354751864e+00  2.977362159634933e+00  4.804226829552658e+00  9.182209655823657e+03 
+    3000  1.021622746681649e+00 -5.898542445856487e+00 -6.009151612939077e+00  4.221727087636999e+00  4.586592133535478e+00  9.245164803297535e+03 
+    3500  1.106519160715706e+00 -5.970546432235779e+00 -6.015249245376119e+00  3.866123627527625e+00  4.609433156737818e+00  9.263945750662717e+03 
+    4000  9.930240066865930e-01 -5.912152557873307e+00 -6.025083715886064e+00  4.138611283233161e+00  4.490143097883684e+00  9.294225198089340e+03 
+    4500  9.646555658575586e-01 -6.015677130022131e+00 -6.036721545560821e+00  3.568689708725919e+00  4.447849418089985e+00  9.330138922961722e+03 
+    5000  9.434923165946090e-01 -6.027456548570741e+00 -6.014550053270733e+00  3.565441638398635e+00  4.639552731684967e+00  9.261770624752438e+03 
+    5500  1.026864240931640e+00 -6.061505823962392e+00 -6.019404988381412e+00  3.401241932620071e+00  4.642991445609312e+00  9.276731237911577e+03 
+    6000  9.983312526598234e-01 -5.946349587454857e+00 -5.983050555300542e+00  3.979901469071073e+00  4.769158832244731e+00  9.165087115091061e+03 
+    6500  1.006036143286260e+00 -5.945850544079388e+00 -6.071303751273131e+00  3.946077295974201e+00  4.225705566446658e+00  9.437216768355414e+03 
+    7000  9.981593359539495e-01 -5.990330698910480e+00 -6.037063892399898e+00  3.663774642188439e+00  4.395425413233882e+00  9.331181435130977e+03 
+    7500  9.507280203289744e-01 -5.984730396336532e+00 -5.991644972746507e+00  3.755491186444424e+00  4.715786618671108e+00  9.191404619772287e+03 
+    8000  9.048837157594684e-01 -6.079029085917312e+00 -5.964267902838972e+00  3.230203589004437e+00  4.889180061475951e+00  9.107693071292861e+03 
+    8500  9.883413333994134e-01 -6.002876846326834e+00 -6.011751334719937e+00  3.642240804100097e+00  4.591282118424260e+00  9.253163154010274e+03 
+    9000  1.056758147654552e+00 -6.036760797857792e+00 -6.002535828890329e+00  3.520846457975964e+00  4.717371526083967e+00  9.224856128595033e+03 
+    9500  1.035347515567710e+00 -5.969647617813958e+00 -5.990309632036265e+00  3.813299824718261e+00  4.694655341617407e+00  9.187302608800977e+03 
+   10000  1.023738343179159e+00 -5.877099589117778e+00 -6.048562900734738e+00  4.344908960531808e+00  4.360340091365503e+00  9.366720846528935e+03 
+   10500  1.069815794809561e+00 -5.913367214053245e+00 -6.010777075880958e+00  4.147089675758311e+00  4.587747175016184e+00  9.250158711907829e+03 
+   11000  9.776294387160251e-01 -5.925772082085378e+00 -5.989277934483906e+00  4.082344757077178e+00  4.717684325105934e+00  9.184160813848264e+03 
+   11500  9.499730095716009e-01 -5.976861040295939e+00 -6.004120411932708e+00  3.808317456317362e+00  4.651789926004906e+00  9.229684845202884e+03 
+   12000  9.782073857977380e-01 -6.066220802750934e+00 -6.031270148041170e+00  3.304122260466307e+00  4.504814328406108e+00  9.313293791801259e+03 
+   12500  9.552683271823048e-01 -6.108551273751968e+00 -5.979666568626595e+00  3.136478232915417e+00  4.876554154588973e+00  9.154740057331765e+03 
+   13000  8.742841944497640e-01 -6.013421944223564e+00 -6.021450865532995e+00  3.577734470946406e+00  4.531631162316097e+00  9.283015239817061e+03 
+   13500  1.004344955842980e+00 -5.899309998559693e+00 -6.011273141389537e+00  4.232629792927130e+00  4.589720100557810e+00  9.251678010621874e+03 
+   14000  9.987696680587935e-01 -5.929715246484374e+00 -6.008152969607664e+00  4.103967501967555e+00  4.653565957595201e+00  9.242036851405348e+03 
+   14500  1.006604156366316e+00 -6.153189106822779e+00 -5.973434451881044e+00  2.841124235115949e+00  4.873303280734345e+00  9.135699098879228e+03 
+   15000  9.051321416654020e-01 -6.031733280212374e+00 -5.972657495662279e+00  3.559001586802186e+00  4.898223883636946e+00  9.133297115127007e+03 
+   15500  9.682672962081463e-01 -6.067136130017134e+00 -5.966412476549884e+00  3.354912150470541e+00  4.933282955614485e+00  9.114211079881910e+03 
+   16000  1.015665897061745e+00 -6.059784334366720e+00 -5.980063616786515e+00  3.369338836061829e+00  4.827107533148539e+00  9.155963314807441e+03 
+   16500  1.006968180883997e+00 -5.995526549328130e+00 -5.964005551783969e+00  3.802449041277696e+00  4.983447487034876e+00  9.106875404577086e+03 
+   17000  1.042050305358167e+00 -5.919486263379956e+00 -6.013086895161285e+00  4.122119914992582e+00  4.584650602653237e+00  9.257241816102296e+03 
+   17500  1.013492134662422e+00 -5.898786232899295e+00 -5.988108507110901e+00  4.246935217818169e+00  4.734032896717861e+00  9.180541556032720e+03 
+   18000  1.045293495070465e+00 -6.013155802624135e+00 -6.000945960251793e+00  3.631220305239846e+00  4.701331109608827e+00  9.219959027336774e+03 
+   18500  9.134705431704426e-01 -5.943263213107316e+00 -6.036334213909798e+00  4.028889501874485e+00  4.494461412575806e+00  9.328923769735196e+03 
+   19000  1.007628738828841e+00 -6.062647924602851e+00 -5.961993496778848e+00  3.347669071096405e+00  4.925642371884200e+00  9.100752827583676e+03 
+   19500  1.000237087620137e+00 -5.934759822585448e+00 -6.020766118588664e+00  4.035509558295610e+00  4.541648097213850e+00  9.280908870426259e+03 
+   20000  9.615364955745067e-01 -5.859940462234714e+00 -5.981549364677676e+00  4.480555066266412e+00  4.782257929522093e+00  9.160435351560425e+03 
+Loop time of 33.5763 on 1 procs for 20000 steps with 256 atoms
+
+Performance: 257324.049 tau/day, 595.658 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 30.404     | 30.404     | 30.404     |   0.0 | 90.55
+Neigh   | 2.1959     | 2.1959     | 2.1959     |   0.0 |  6.54
+Comm    | 0.50746    | 0.50746    | 0.50746    |   0.0 |  1.51
+Output  | 0.16503    | 0.16503    | 0.16503    |   0.0 |  0.49
+Modify  | 0.237      | 0.237      | 0.237      |   0.0 |  0.71
+Other   |            | 0.06721    |            |       |  0.20
+
+Nlocal:    256 ave 256 max 256 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2116 ave 2116 max 2116 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    19135 ave 19135 max 19135 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19135
+Ave neighs/atom = 74.7461
+Neighbor list builds = 1946
+Dangerous builds = 1902
+thermo 20
+run 200000
+Per MPI rank memory allocation (min/avg/max) = 3.806 | 3.806 | 3.806 Mbytes
+Elapsed Temp c_u c_hma[1] c_p c_hma[2] c_hma[3] 
+       0  9.615364955745067e-01 -5.859940462234714e+00 -5.981549364677676e+00  4.480555066266412e+00  4.782257929522093e+00  9.160435351560425e+03 
+      20  1.020600011999315e+00 -5.958432657247554e+00 -5.970407876039725e+00  3.888068459330918e+00  4.819304899867157e+00  9.126408714227488e+03 
+      40  9.814651761832457e-01 -5.909251537070915e+00 -5.991660882363840e+00  4.211003703521785e+00  4.737796490044842e+00  9.191407419668969e+03 
+      60  1.017977787037964e+00 -5.969196214125930e+00 -5.964268442742594e+00  3.868843363187895e+00  4.897139389041168e+00  9.107658398968413e+03 
+      80  1.014099325641110e+00 -5.967528512390698e+00 -5.995071997895454e+00  3.830673462482372e+00  4.672514506373457e+00  9.201917832597679e+03 
+     100  9.996875356603929e-01 -5.951588326170250e+00 -6.038052192222564e+00  3.956276886785969e+00  4.459787987673556e+00  9.334249364612955e+03 
+     120  1.012056868305871e+00 -5.978870473165807e+00 -6.025850442982817e+00  3.772945936859251e+00  4.503179680043147e+00  9.296565936440789e+03 
+     140  9.767869134157122e-01 -5.935832220940478e+00 -5.962749498947353e+00  4.000315968594315e+00  4.845752792843529e+00  9.103038302449055e+03 
+     160  9.892523056702491e-01 -5.959324837828405e+00 -5.989985114179447e+00  3.844041265550217e+00  4.667985214080106e+00  9.186300645060488e+03 
+     180  9.515078978028194e-01 -5.906073543975624e+00 -5.989405874738726e+00  4.168541295586040e+00  4.690034156707802e+00  9.184525321314130e+03 
+     200  9.472636015419604e-01 -5.901747840949999e+00 -6.059197474754500e+00  4.085216465358702e+00  4.181116302801172e+00  9.399653985979861e+03 
+     220  9.987356397412785e-01 -5.979817989736361e+00 -6.023113896710152e+00  3.732212025258467e+00  4.483600227395010e+00  9.288140153203587e+03 
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+  199380  1.045345255275729e+00 -6.054903517585581e+00 -6.000275517756035e+00  3.428601172163945e+00  4.742283600840854e+00  9.217917022324442e+03 
+  199400  9.780104923920887e-01 -5.958423420917970e+00 -6.016396141193878e+00  3.865736483935700e+00  4.532848152861964e+00  9.267458321744127e+03 
+  199420  9.694306975833765e-01 -5.949393899958658e+00 -6.034676514495618e+00  3.942958172837187e+00  4.453252202724016e+00  9.323803532354184e+03 
+  199440  1.011138230619257e+00 -6.015121038088004e+00 -6.009321354178946e+00  3.625230601241597e+00  4.658533283745596e+00  9.245682356743368e+03 
+  199460  9.823835158722997e-01 -5.976377539506453e+00 -6.001894201937834e+00  3.798620426431028e+00  4.652099802059292e+00  9.222862453835854e+03 
+  199480  1.074562355574544e+00 -6.118486926125487e+00 -5.995296473648373e+00  3.016297520865714e+00  4.723676162650218e+00  9.202624643333613e+03 
+  199500  9.926831596967829e-01 -6.005199868966562e+00 -6.000357663445108e+00  3.700903545492443e+00  4.728708238925513e+00  9.218133858751144e+03 
+  199520  9.528151168241586e-01 -5.959418705000071e+00 -5.963065830859622e+00  3.901076693474031e+00  4.880134332397586e+00  9.104004014073711e+03 
+  199540  9.557829809703990e-01 -5.977637161975556e+00 -5.991671870257975e+00  3.799602485859072e+00  4.719013019037336e+00  9.191491214806965e+03 
+  199560  9.838846370790553e-01 -6.036655642150919e+00 -6.003509719541851e+00  3.458439215320582e+00  4.648768232256796e+00  9.227830722879620e+03 
+  199580  9.843932648042784e-01 -6.058662065699025e+00 -6.020554801397395e+00  3.374629497019970e+00  4.593447305720019e+00  9.280268165956993e+03 
+  199600  1.065184573658751e+00 -6.206851690895959e+00 -5.968086425263754e+00  2.610633649932813e+00  4.981660753998377e+00  9.119370099006041e+03 
+  199620  9.388817486791809e-01 -6.048259703771625e+00 -6.004812660448888e+00  3.444013103007198e+00  4.693492749174577e+00  9.231822964740768e+03 
+  199640  9.473654082682319e-01 -6.087966531003856e+00 -5.979134478052076e+00  3.195402416940680e+00  4.820332906695564e+00  9.153129876030411e+03 
+  199660  9.210577256459164e-01 -6.068236326393697e+00 -5.967782053655758e+00  3.335152873111248e+00  4.911976852420958e+00  9.118414230427796e+03 
+  199680  9.497229600007705e-01 -6.121910609110069e+00 -5.971990252219380e+00  3.092920192420396e+00  4.953786081786985e+00  9.131271875339731e+03 
+  199700  9.516524276659803e-01 -6.127906301058084e+00 -6.000100462469979e+00  2.979286429490728e+00  4.713167332553232e+00  9.217372102518229e+03 
+  199720  9.443608833647245e-01 -6.114016019953694e+00 -6.000580190700743e+00  3.091035310234930e+00  4.742401395943221e+00  9.218828712551509e+03 
+  199740  8.681959517945045e-01 -5.990991490549361e+00 -5.977120027277696e+00  3.797772807366312e+00  4.877424896074221e+00  9.146908120580996e+03 
+  199760  9.625155118642070e-01 -6.110458936060956e+00 -5.978494259332300e+00  3.124357089378134e+00  4.882118684621803e+00  9.151154400341169e+03 
+  199780  9.848261985222230e-01 -6.112095588872020e+00 -5.980370944143631e+00  3.096964062230267e+00  4.853347356583562e+00  9.156887038258950e+03 
+  199800  9.658504385268453e-01 -6.044741959287682e+00 -5.983150214559801e+00  3.514935168261291e+00  4.868604497780478e+00  9.165405595380049e+03 
+  199820  9.830751481829464e-01 -6.030277382849008e+00 -6.003547531492968e+00  3.595906231692601e+00  4.749393174610113e+00  9.227958060577354e+03 
+  199840  1.019195363692946e+00 -6.047159382563301e+00 -6.018232273751166e+00  3.484691277977978e+00  4.650795213232877e+00  9.273127872675630e+03 
+  199860  1.009814556481902e+00 -6.004451936660288e+00 -6.029796701673096e+00  3.664786858860082e+00  4.519253296066829e+00  9.308739911114350e+03 
+  199880  1.004112823631311e+00 -5.975808665464897e+00 -5.994508893678078e+00  3.866906624242725e+00  4.759527019991680e+00  9.200211087352904e+03 
+  199900  1.017006687798344e+00 -5.979166475348716e+00 -6.024287631510320e+00  3.884200204963863e+00  4.625107543807584e+00  9.291749564292193e+03 
+  199920  1.029645300704506e+00 -5.988407957108219e+00 -6.015604824463416e+00  3.792038397567344e+00  4.635869776512177e+00  9.265017077501841e+03 
+  199940  1.016090771897235e+00 -5.963111834339648e+00 -5.964819076856839e+00  3.924983490607407e+00  4.915180239878768e+00  9.109359800541135e+03 
+  199960  1.089150523107765e+00 -6.068080542656683e+00 -5.972503306663688e+00  3.396420435709163e+00  4.945239715310409e+00  9.132824214410233e+03 
+  199980  9.700833243472550e-01 -5.891585904890412e+00 -6.005450837672986e+00  4.354796401538968e+00  4.700966336960025e+00  9.233789429481529e+03 
+  200000  1.036656071639917e+00 -5.992403506639822e+00 -5.993257960485003e+00  3.764547892583718e+00  4.759641486378383e+00  9.196316925648398e+03 
+Loop time of 380.886 on 1 procs for 200000 steps with 256 atoms
+
+Performance: 226839.823 tau/day, 525.092 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 308.99     | 308.99     | 308.99     |   0.0 | 81.12
+Neigh   | 22.559     | 22.559     | 22.559     |   0.0 |  5.92
+Comm    | 5.1164     | 5.1164     | 5.1164     |   0.0 |  1.34
+Output  | 41.166     | 41.166     | 41.166     |   0.0 | 10.81
+Modify  | 2.379      | 2.379      | 2.379      |   0.0 |  0.62
+Other   |            | 0.6754     |            |       |  0.18
+
+Nlocal:    256 ave 256 max 256 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2125 ave 2125 max 2125 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    19131 ave 19131 max 19131 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19131
+Ave neighs/atom = 74.7305
+Neighbor list builds = 19989
+Dangerous builds = 19886
+Total wall time: 0:06:54
diff --git a/examples/USER/misc/hma/log.6Nov18.hma.g++.4 b/examples/USER/misc/hma/log.6Nov18.hma.g++.4
new file mode 100644
index 0000000000..5b25fa5cf5
--- /dev/null
+++ b/examples/USER/misc/hma/log.6Nov18.hma.g++.4
@@ -0,0 +1,10159 @@
+LAMMPS (31 Aug 2018)
+# Harmonically mapped average example
+
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+atom_modify map array
+# ---------- Create Atoms ----------------------------
+lattice 	fcc 1.0
+Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
+region	box block 0 4 0 4 0 4 units lattice
+create_box	1 box
+Created orthogonal box = (0 0 0) to (6.3496 6.3496 6.3496)
+  1 by 2 by 2 MPI processor grid
+lattice	fcc 1.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
+Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
+create_atoms 1 region box
+Created 256 atoms
+  Time spent = 0.000636816 secs
+# ---------- Define Interatomic Potential ---------------------
+pair_style lj/smooth/linear 3
+pair_coeff * * 1.0 1.0
+mass 1 1.0
+
+atom_modify sort 0 1
+velocity all create 0.1 45678 dist gaussian
+
+compute u all pe
+
+compute p all pressure NULL pair
+
+compute hma all HMA settemp u p 9.579586686264458 cv
+
+timestep 0.005
+
+fix settemp all nvt temp 1.0 1.0 0.5
+thermo_style custom elapsed temp c_u c_hma[1] c_p c_hma[2] c_hma[3]
+thermo_modify format float '%22.15e'
+thermo 500
+run 20000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.3
+  ghost atom cutoff = 3.3
+  binsize = 1.65, bins = 4 4 4
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/smooth/linear, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute HMA, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.389 | 3.389 | 3.389 Mbytes
+Elapsed Temp c_u c_hma[1] c_p c_hma[2] c_hma[3] 
+       0  9.999999999999999e-02 -7.321210550030622e+00 -5.827069925030622e+00 -3.541123363606526e+00  6.038463322657932e+00  8.693908581891272e+03 
+     500  2.319904532047116e-01 -7.021814067268549e+00 -5.841520703728273e+00 -1.859554996730893e+00  5.917872146525079e+00  8.737041016754241e+03 
+    1000  1.104889191155021e+00 -6.005326544560477e+00 -6.005300065747159e+00  3.645694884120414e+00  4.645846929564070e+00  9.233336265503700e+03 
+    1500  9.475049376144361e-01 -6.133389836457317e+00 -5.983811791861923e+00  2.980778280706599e+00  4.839678559900945e+00  9.167450093661304e+03 
+    2000  9.009354935012601e-01 -6.066361566415782e+00 -5.975649385751911e+00  3.331919983683387e+00  4.852803362719920e+00  9.142450653666589e+03 
+    2500  1.002748731362028e+00 -6.037709705055500e+00 -5.998660236350431e+00  3.517524667487255e+00  4.741752759677512e+00  9.212938381713899e+03 
+    3000  1.123087652951704e+00 -6.025819107168451e+00 -5.970493239986080e+00  3.598743028856235e+00  4.916432719867683e+00  9.126676463986189e+03 
+    3500  1.115128009750835e+00 -6.000529470165528e+00 -5.980015761414576e+00  3.665878335379198e+00  4.783671225513338e+00  9.155782280210480e+03 
+    4000  9.904879689205039e-01 -5.990830917252424e+00 -6.007049321999301e+00  3.700324729502504e+00  4.607196139655914e+00  9.238716127101230e+03 
+    4500  9.696423790018132e-01 -6.095364960235830e+00 -5.949103254372231e+00  3.188999551316120e+00  5.028856900310743e+00  9.061471896280929e+03 
+    5000  1.005681297563624e+00 -6.094938179693363e+00 -6.014945551672039e+00  3.140253069724724e+00  4.599583118642348e+00  9.263005212755274e+03 
+    5500  1.067821663160412e+00 -6.055271652935048e+00 -6.039553220002009e+00  3.350955211546091e+00  4.441212885867230e+00  9.338870121131475e+03 
+    6000  1.019349023817732e+00 -5.912735006243721e+00 -6.010199997355059e+00  4.160148455119939e+00  4.600489393500003e+00  9.248369562541713e+03 
+    6500  1.033977564076081e+00 -5.962511500402099e+00 -5.953097811556573e+00  3.913955620678704e+00  4.968010478793357e+00  9.073605525336026e+03 
+    7000  1.035036973336388e+00 -6.011513860495915e+00 -5.988661036457318e+00  3.570585392636366e+00  4.701809844729083e+00  9.182284012600518e+03 
+    7500  9.759766417830451e-01 -6.011014245515786e+00 -5.997095489328838e+00  3.659421763886547e+00  4.739345415832561e+00  9.208142257833988e+03 
+    8000  9.701274032979823e-01 -6.070706464001116e+00 -5.987899394187518e+00  3.293522632549048e+00  4.769013641771370e+00  9.179944973040452e+03 
+    8500  1.002959574283594e+00 -6.000331246180245e+00 -6.022939013616290e+00  3.707537441996905e+00  4.577720142838428e+00  9.287619492673581e+03 
+    9000  9.541471061067928e-01 -5.891837375294362e+00 -6.000893913894259e+00  4.214373867383508e+00  4.588154346298096e+00  9.219760426705488e+03 
+    9500  1.005476043930556e+00 -6.054397260431607e+00 -5.963822185829731e+00  3.425817325831102e+00  4.945913420642570e+00  9.106317976320150e+03 
+   10000  9.834510517532772e-01 -5.979858570968017e+00 -6.007829122692488e+00  3.832487507111145e+00  4.671876270680338e+00  9.241093007564954e+03 
+   10500  1.053423257346257e+00 -5.984863687481322e+00 -5.990560458118040e+00  3.742155897948207e+00  4.709444159379769e+00  9.188099433599265e+03 
+   11000  1.027766819783240e+00 -5.964303012082833e+00 -5.987340607292543e+00  3.942276092974025e+00  4.809990656223532e+00  9.178213465454402e+03 
+   11500  1.030919611642090e+00 -5.996031790431708e+00 -6.010813071174461e+00  3.713452645350145e+00  4.628576243929453e+00  9.250277317464830e+03 
+   12000  1.015499044847646e+00 -5.983611533298556e+00 -6.000577066405612e+00  3.747611330243804e+00  4.650192613735324e+00  9.218807640515772e+03 
+   12500  9.260784226173562e-01 -5.995616138164384e+00 -6.024603077235440e+00  3.708688522431407e+00  4.542241032571079e+00  9.292727745364478e+03 
+   13000  9.581084725650251e-01 -6.095817502268568e+00 -5.989303506622369e+00  3.230806633332333e+00  4.842426479320365e+00  9.184229513868806e+03 
+   13500  9.246476920572243e-01 -5.986197290479123e+00 -5.980486024616446e+00  3.778398028002328e+00  4.811193000401358e+00  9.157208321147285e+03 
+   14000  9.018834156590910e-01 -5.891981523518482e+00 -5.961281643266227e+00  4.310640039569481e+00  4.912708027819059e+00  9.098571305044385e+03 
+   14500  9.458192412990540e-01 -5.924212527125402e+00 -5.974831040418032e+00  4.099524287456710e+00  4.808864950940809e+00  9.139925423823777e+03 
+   15000  1.079258475602827e+00 -5.842389291052847e+00 -5.997594135488276e+00  4.542013464261510e+00  4.650803229641226e+00  9.209631946001080e+03 
+   15500  1.003773905363782e+00 -5.990536501227417e+00 -5.978949148782005e+00  3.711448614654375e+00  4.777984985532921e+00  9.152543385133793e+03 
+   16000  9.589971646383746e-01 -6.022404990638810e+00 -6.013121691584658e+00  3.591520611305744e+00  4.644826751060574e+00  9.257382394405931e+03 
+   16500  1.027873542611377e+00 -6.062068879792612e+00 -5.995808570227100e+00  3.344041739290934e+00  4.724518690565871e+00  9.204185610519249e+03 
+   17000  9.721883229756479e-01 -6.076377536863534e+00 -5.995495525201934e+00  3.317173564950596e+00  4.781610592362355e+00  9.203227919920830e+03 
+   17500  9.870692120707141e-01 -5.965983792560558e+00 -6.036111701999152e+00  3.838886592024325e+00  4.436201283769008e+00  9.328234074356338e+03 
+   18000  1.004272604822617e+00 -5.960763698221652e+00 -5.980795290630440e+00  3.950710186832507e+00  4.835685683342340e+00  9.158184493996429e+03 
+   18500  9.381056200232580e-01 -5.953631223909241e+00 -6.011057530919335e+00  3.898044457090124e+00  4.568293715545873e+00  9.251034889270257e+03 
+   19000  9.369931263537112e-01 -6.012014674095721e+00 -5.987682214265706e+00  3.582518713971043e+00  4.722239463750979e+00  9.179299635700279e+03 
+   19500  9.837184187823201e-01 -5.957066902345472e+00 -6.012125787465584e+00  3.937810342708973e+00  4.621653704014352e+00  9.254320960371275e+03 
+   20000  1.079101865720838e+00 -6.089503178102808e+00 -5.960131548856806e+00  3.215696838220799e+00  4.958568753546265e+00  9.095068306811330e+03 
+Loop time of 4.841 on 4 procs for 20000 steps with 256 atoms
+
+Performance: 1784755.120 tau/day, 4131.378 timesteps/s
+98.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.3889     | 2.6923     | 3.0228     |  14.4 | 55.62
+Neigh   | 0.52899    | 0.5489     | 0.57081    |   2.3 | 11.34
+Comm    | 1.0419     | 1.3856     | 1.697      |  20.8 | 28.62
+Output  | 0.022234   | 0.022308   | 0.022518   |   0.1 |  0.46
+Modify  | 0.13626    | 0.14418    | 0.15704    |   2.2 |  2.98
+Other   |            | 0.04763    |            |       |  0.98
+
+Nlocal:    64 ave 68 max 60 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:    1344.25 ave 1352 max 1339 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Neighs:    4758 ave 5243 max 3935 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+
+Total # of neighbors = 19032
+Ave neighs/atom = 74.3438
+Neighbor list builds = 1938
+Dangerous builds = 1898
+thermo 20
+run 200000
+Per MPI rank memory allocation (min/avg/max) = 3.771 | 3.771 | 3.771 Mbytes
+Elapsed Temp c_u c_hma[1] c_p c_hma[2] c_hma[3] 
+       0  1.079101865720838e+00 -6.089503178102806e+00 -5.960131548856804e+00  3.215696838220800e+00  4.958568753546269e+00  9.095068306811325e+03 
+      20  1.045882952900159e+00 -6.018338283555533e+00 -5.972366139305224e+00  3.616958874311578e+00  4.880938040763178e+00  9.132383004784513e+03 
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+  199180  9.461899773815526e-01 -6.032973235700828e+00 -6.002627685618304e+00  3.540355763785038e+00  4.714604608317587e+00  9.225128874167300e+03 
+  199200  9.169446904375247e-01 -6.019126632617641e+00 -5.997209799086605e+00  3.576319367836887e+00  4.702169217591129e+00  9.208489636133518e+03 
+  199220  9.655191552051936e-01 -6.113552120495919e+00 -5.926744209665422e+00  3.125824757962981e+00  5.198504690382469e+00  8.993547436383958e+03 
+  199240  9.657417036500927e-01 -6.125677031988027e+00 -5.954581422156043e+00  3.056385820498082e+00  5.038843289113387e+00  9.078160732826180e+03 
+  199260  9.877273315555719e-01 -6.163001810414066e+00 -5.990981509760339e+00  2.781671000552668e+00  4.769438186961859e+00  9.189401612365369e+03 
+  199280  9.164016537739427e-01 -6.057427989294474e+00 -5.970006140233552e+00  3.394534142724440e+00  4.896523928519669e+00  9.125220781308743e+03 
+  199300  9.474448171313214e-01 -6.095091760743020e+00 -5.982569132614822e+00  3.191877067034992e+00  4.837999410567528e+00  9.163618069188802e+03 
+  199320  9.825702308519964e-01 -6.129777319180471e+00 -5.984787297986816e+00  2.983357250828027e+00  4.815912389655264e+00  9.170418953085722e+03 
+  199340  9.233561907968878e-01 -6.017889690848733e+00 -5.983733303433910e+00  3.630539129044245e+00  4.826670391264030e+00  9.167180137520203e+03 
+  199360  9.833446666705657e-01 -6.071562030718987e+00 -6.002138341950408e+00  3.277238656398008e+00  4.675880220588303e+00  9.223623351935497e+03 
+  199380  9.904879622213187e-01 -6.041612705995380e+00 -5.977971123946595e+00  3.543101385561040e+00  4.908541198188153e+00  9.149553915048507e+03 
+  199400  9.531451151255562e-01 -5.944451955308232e+00 -6.020145704520475e+00  4.020207021150083e+00  4.585561799603552e+00  9.278986391660319e+03 
+  199420  9.302501168049160e-01 -5.876127504871770e+00 -6.031229636167053e+00  4.436552729181573e+00  4.545932289306807e+00  9.313163269864563e+03 
+  199440  1.067356731062996e+00 -6.053025969964114e+00 -6.001881800622634e+00  3.418665160248135e+00  4.712342895141543e+00  9.222807297010597e+03 
+  199460  1.049510899882768e+00 -6.009171098342096e+00 -5.962259422337160e+00  3.655704219850209e+00  4.925078323028947e+00  9.101565195316367e+03 
+  199480  1.044519255577664e+00 -5.992229978207050e+00 -6.049878297079360e+00  3.710885987918348e+00  4.379860419905029e+00  9.370786156864542e+03 
+  199500  9.847609446149433e-01 -5.900903108064672e+00 -6.017893280075429e+00  4.252555905378914e+00  4.580780233522542e+00  9.272040626800444e+03 
+  199520  9.726026013727151e-01 -5.881495003585851e+00 -6.036443208744220e+00  4.348750297248522e+00  4.459013725071912e+00  9.329243017857832e+03 
+  199540  1.010034818694413e+00 -5.940409035620492e+00 -6.038026222552443e+00  4.013419066226046e+00  4.452886072651932e+00  9.334132119631533e+03 
+  199560  1.040614778341884e+00 -5.991255001091267e+00 -6.014165865584546e+00  3.761870949825876e+00  4.630313220460650e+00  9.260570532384259e+03 
+  199580  9.876228168731374e-01 -5.920005727090434e+00 -5.986205024750682e+00  4.158082425501370e+00  4.777955814028018e+00  9.174758238441040e+03 
+  199600  1.012865828224957e+00 -5.965936366697965e+00 -5.983591445494183e+00  3.864537565495610e+00  4.763159370933115e+00  9.166728018144922e+03 
+  199620  9.781413945744000e-01 -5.923538991148838e+00 -5.969799366321246e+00  4.156505310912000e+00  4.890871077902111e+00  9.124570404367860e+03 
+  199640  1.099765286334250e+00 -6.114689303161841e+00 -5.986635051507113e+00  3.117695888685802e+00  4.853003218018651e+00  9.176076291045239e+03 
+  199660  9.733540898763735e-01 -5.943014965150123e+00 -6.026748203311058e+00  3.953333946392712e+00  4.472524735195893e+00  9.299371258522997e+03 
+  199680  1.020419325781833e+00 -6.029875926956803e+00 -6.008154673470141e+00  3.556826355567539e+00  4.681553154441065e+00  9.242086748417116e+03 
+  199700  9.810593732039271e-01 -5.990291462713761e+00 -5.967726450473815e+00  3.744230860893893e+00  4.873802653100023e+00  9.118263504756900e+03 
+  199720  9.784782707049126e-01 -6.006654552718952e+00 -5.985793021212336e+00  3.668265940296609e+00  4.788056082519161e+00  9.173492287727226e+03 
+  199740  9.418235269606751e-01 -5.974755483458068e+00 -6.013514831715964e+00  3.892227035818223e+00  4.669664860131629e+00  9.258555704354141e+03 
+  199760  9.832394135578619e-01 -6.060661637263619e+00 -6.009626350201415e+00  3.325320325409244e+00  4.618372841405569e+00  9.246627143084354e+03 
+  199780  9.498194638281705e-01 -6.035882868576457e+00 -6.000101480557392e+00  3.474210718137948e+00  4.679672985295322e+00  9.217356306124026e+03 
+  199800  9.583864529664586e-01 -6.076119003394955e+00 -6.009708957467579e+00  3.242593120679117e+00  4.623929881315505e+00  9.246899990826470e+03 
+  199820  9.904273190776074e-01 -6.154404000245639e+00 -5.941030166708029e+00  2.909664010944320e+00  5.134889582611303e+00  9.036909661193709e+03 
+  199840  9.102207622852591e-01 -6.065663616522880e+00 -5.978347946184162e+00  3.372945213680421e+00  4.874325304821653e+00  9.150648183986643e+03 
+  199860  8.494642503362303e-01 -6.001629984670598e+00 -6.000908287105964e+00  3.689399501675942e+00  4.693543600774409e+00  9.219824648728385e+03 
+  199880  9.124194373292649e-01 -6.115327755301041e+00 -6.013664364930694e+00  3.022386552368757e+00  4.606153472234109e+00  9.259048264012663e+03 
+  199900  9.012855081825699e-01 -6.115355873351151e+00 -5.968200087682216e+00  3.132786366069281e+00  4.977777659664543e+00  9.119696429693091e+03 
+  199920  8.478880513404523e-01 -6.043267344699284e+00 -5.977625330208900e+00  3.500506679661614e+00  4.877433284934312e+00  9.148497479033846e+03 
+  199940  8.660608083304254e-01 -6.064289496109857e+00 -6.010313559354831e+00  3.416172307521693e+00  4.726110489118270e+00  9.248739882428541e+03 
+  199960  9.304301216794905e-01 -6.139891398497096e+00 -5.977879919520982e+00  3.023079698606037e+00  4.953374682082232e+00  9.149294637624478e+03 
+  199980  9.633635787878904e-01 -6.153324116670857e+00 -5.981484082093043e+00  2.878934939218798e+00  4.865667009924017e+00  9.160317920496162e+03 
+  200000  9.635163730977483e-01 -6.102203225911095e+00 -5.997212004084306e+00  3.191924486932165e+00  4.794800330000662e+00  9.208486378845661e+03 
+Loop time of 56.3641 on 4 procs for 200000 steps with 256 atoms
+
+Performance: 1532891.800 tau/day, 3548.361 timesteps/s
+98.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 25.291     | 28.255     | 31.464     |  44.1 | 50.13
+Neigh   | 5.5169     | 5.6888     | 5.8734     |   6.9 | 10.09
+Comm    | 11.506     | 14.839     | 17.828     |  63.0 | 26.33
+Output  | 5.5139     | 5.5345     | 5.5859     |   1.3 |  9.82
+Modify  | 1.4354     | 1.497      | 1.6066     |   5.6 |  2.66
+Other   |            | 0.5505     |            |       |  0.98
+
+Nlocal:    64 ave 65 max 63 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    1334.5 ave 1343 max 1328 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs:    4748.25 ave 5438 max 4111 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+
+Total # of neighbors = 18993
+Ave neighs/atom = 74.1914
+Neighbor list builds = 19989
+Dangerous builds = 19885
+Total wall time: 0:01:01
diff --git a/examples/USER/misc/ilp_graphene_hbn/Bi_gr_AB_stack_2L_noH.data b/examples/USER/misc/ilp_graphene_hbn/Bi_gr_AB_stack_2L_noH.data
new file mode 100644
index 0000000000..756123a6f1
--- /dev/null
+++ b/examples/USER/misc/ilp_graphene_hbn/Bi_gr_AB_stack_2L_noH.data
@@ -0,0 +1,1372 @@
+ Generate Bi-layer graphene
+
+   1360  atoms
+
+ 2 atom types
+
+    0.000000000000000  42.599999999999994 xlo xhi
+    0.000000000000000  41.811706494712695 ylo yhi
+    0.000000000000000 100.000000000000000 zlo zhi
+
+ Atoms
+
+          1         1         1   0.000000000000000   0.000000000000000   1.229756073373903   0.000000000000000
+          2         1         1   0.000000000000000   0.710000000000000   0.000000000000000   0.000000000000000
+          3         1         1   0.000000000000000   2.130000000000000   0.000000000000000   0.000000000000000
+          4         1         1   0.000000000000000   2.840000000000000   1.229756073373903   0.000000000000000
+          5         1         1   0.000000000000000   4.260000000000000   1.229756073373903   0.000000000000000
+          6         1         1   0.000000000000000   4.970000000000000   0.000000000000000   0.000000000000000
+          7         1         1   0.000000000000000   6.390000000000000   0.000000000000000   0.000000000000000
+          8         1         1   0.000000000000000   7.100000000000000   1.229756073373903   0.000000000000000
+          9         1         1   0.000000000000000   8.520000000000000   1.229756073373903   0.000000000000000
+         10         1         1   0.000000000000000   9.230000000000000   0.000000000000000   0.000000000000000
+         11         1         1   0.000000000000000  10.649999999999999   0.000000000000000   0.000000000000000
+         12         1         1   0.000000000000000  11.359999999999999   1.229756073373903   0.000000000000000
+         13         1         1   0.000000000000000  12.779999999999999   1.229756073373903   0.000000000000000
+         14         1         1   0.000000000000000  13.489999999999998   0.000000000000000   0.000000000000000
+         15         1         1   0.000000000000000  14.910000000000000   0.000000000000000   0.000000000000000
+         16         1         1   0.000000000000000  15.619999999999999   1.229756073373903   0.000000000000000
+         17         1         1   0.000000000000000  17.039999999999999   1.229756073373903   0.000000000000000
+         18         1         1   0.000000000000000  17.750000000000000   0.000000000000000   0.000000000000000
+         19         1         1   0.000000000000000  19.169999999999998   0.000000000000000   0.000000000000000
+         20         1         1   0.000000000000000  19.879999999999999   1.229756073373903   0.000000000000000
+         21         1         1   0.000000000000000  21.299999999999997   1.229756073373903   0.000000000000000
+         22         1         1   0.000000000000000  22.009999999999998   0.000000000000000   0.000000000000000
+         23         1         1   0.000000000000000  23.429999999999996   0.000000000000000   0.000000000000000
+         24         1         1   0.000000000000000  24.139999999999997   1.229756073373903   0.000000000000000
+         25         1         1   0.000000000000000  25.559999999999999   1.229756073373903   0.000000000000000
+         26         1         1   0.000000000000000  26.270000000000000   0.000000000000000   0.000000000000000
+         27         1         1   0.000000000000000  27.689999999999998   0.000000000000000   0.000000000000000
+         28         1         1   0.000000000000000  28.399999999999999   1.229756073373903   0.000000000000000
+         29         1         1   0.000000000000000  29.820000000000000   1.229756073373903   0.000000000000000
+         30         1         1   0.000000000000000  30.530000000000001   0.000000000000000   0.000000000000000
+         31         1         1   0.000000000000000  31.949999999999999   0.000000000000000   0.000000000000000
+         32         1         1   0.000000000000000  32.659999999999997   1.229756073373903   0.000000000000000
+         33         1         1   0.000000000000000  34.079999999999998   1.229756073373903   0.000000000000000
+         34         1         1   0.000000000000000  34.789999999999999   0.000000000000000   0.000000000000000
+         35         1         1   0.000000000000000  36.210000000000001   0.000000000000000   0.000000000000000
+         36         1         1   0.000000000000000  36.920000000000002   1.229756073373903   0.000000000000000
+         37         1         1   0.000000000000000  38.339999999999996   1.229756073373903   0.000000000000000
+         38         1         1   0.000000000000000  39.049999999999997   0.000000000000000   0.000000000000000
+         39         1         1   0.000000000000000  40.469999999999999   0.000000000000000   0.000000000000000
+         40         1         1   0.000000000000000  41.179999999999993   1.229756073373903   0.000000000000000
+         41         1         1   0.000000000000000   0.000000000000000   3.689268220121709   0.000000000000000
+         42         1         1   0.000000000000000   0.710000000000000   2.459512146747806   0.000000000000000
+         43         1         1   0.000000000000000   2.130000000000000   2.459512146747806   0.000000000000000
+         44         1         1   0.000000000000000   2.840000000000000   3.689268220121709   0.000000000000000
+         45         1         1   0.000000000000000   4.260000000000000   3.689268220121709   0.000000000000000
+         46         1         1   0.000000000000000   4.970000000000000   2.459512146747806   0.000000000000000
+         47         1         1   0.000000000000000   6.390000000000000   2.459512146747806   0.000000000000000
+         48         1         1   0.000000000000000   7.100000000000000   3.689268220121709   0.000000000000000
+         49         1         1   0.000000000000000   8.520000000000000   3.689268220121709   0.000000000000000
+         50         1         1   0.000000000000000   9.230000000000000   2.459512146747806   0.000000000000000
+         51         1         1   0.000000000000000  10.649999999999999   2.459512146747806   0.000000000000000
+         52         1         1   0.000000000000000  11.359999999999999   3.689268220121709   0.000000000000000
+         53         1         1   0.000000000000000  12.779999999999999   3.689268220121709   0.000000000000000
+         54         1         1   0.000000000000000  13.489999999999998   2.459512146747806   0.000000000000000
+         55         1         1   0.000000000000000  14.910000000000000   2.459512146747806   0.000000000000000
+         56         1         1   0.000000000000000  15.619999999999999   3.689268220121709   0.000000000000000
+         57         1         1   0.000000000000000  17.039999999999999   3.689268220121709   0.000000000000000
+         58         1         1   0.000000000000000  17.750000000000000   2.459512146747806   0.000000000000000
+         59         1         1   0.000000000000000  19.169999999999998   2.459512146747806   0.000000000000000
+         60         1         1   0.000000000000000  19.879999999999999   3.689268220121709   0.000000000000000
+         61         1         1   0.000000000000000  21.299999999999997   3.689268220121709   0.000000000000000
+         62         1         1   0.000000000000000  22.009999999999998   2.459512146747806   0.000000000000000
+         63         1         1   0.000000000000000  23.429999999999996   2.459512146747806   0.000000000000000
+         64         1         1   0.000000000000000  24.139999999999997   3.689268220121709   0.000000000000000
+         65         1         1   0.000000000000000  25.559999999999999   3.689268220121709   0.000000000000000
+         66         1         1   0.000000000000000  26.270000000000000   2.459512146747806   0.000000000000000
+         67         1         1   0.000000000000000  27.689999999999998   2.459512146747806   0.000000000000000
+         68         1         1   0.000000000000000  28.399999999999999   3.689268220121709   0.000000000000000
+         69         1         1   0.000000000000000  29.820000000000000   3.689268220121709   0.000000000000000
+         70         1         1   0.000000000000000  30.530000000000001   2.459512146747806   0.000000000000000
+         71         1         1   0.000000000000000  31.949999999999999   2.459512146747806   0.000000000000000
+         72         1         1   0.000000000000000  32.659999999999997   3.689268220121709   0.000000000000000
+         73         1         1   0.000000000000000  34.079999999999998   3.689268220121709   0.000000000000000
+         74         1         1   0.000000000000000  34.789999999999999   2.459512146747806   0.000000000000000
+         75         1         1   0.000000000000000  36.210000000000001   2.459512146747806   0.000000000000000
+         76         1         1   0.000000000000000  36.920000000000002   3.689268220121709   0.000000000000000
+         77         1         1   0.000000000000000  38.339999999999996   3.689268220121709   0.000000000000000
+         78         1         1   0.000000000000000  39.049999999999997   2.459512146747806   0.000000000000000
+         79         1         1   0.000000000000000  40.469999999999999   2.459512146747806   0.000000000000000
+         80         1         1   0.000000000000000  41.179999999999993   3.689268220121709   0.000000000000000
+         81         1         1   0.000000000000000   0.000000000000000   6.148780366869514   0.000000000000000
+         82         1         1   0.000000000000000   0.710000000000000   4.919024293495611   0.000000000000000
+         83         1         1   0.000000000000000   2.130000000000000   4.919024293495611   0.000000000000000
+         84         1         1   0.000000000000000   2.840000000000000   6.148780366869514   0.000000000000000
+         85         1         1   0.000000000000000   4.260000000000000   6.148780366869514   0.000000000000000
+         86         1         1   0.000000000000000   4.970000000000000   4.919024293495611   0.000000000000000
+         87         1         1   0.000000000000000   6.390000000000000   4.919024293495611   0.000000000000000
+         88         1         1   0.000000000000000   7.100000000000000   6.148780366869514   0.000000000000000
+         89         1         1   0.000000000000000   8.520000000000000   6.148780366869514   0.000000000000000
+         90         1         1   0.000000000000000   9.230000000000000   4.919024293495611   0.000000000000000
+         91         1         1   0.000000000000000  10.649999999999999   4.919024293495611   0.000000000000000
+         92         1         1   0.000000000000000  11.359999999999999   6.148780366869514   0.000000000000000
+         93         1         1   0.000000000000000  12.779999999999999   6.148780366869514   0.000000000000000
+         94         1         1   0.000000000000000  13.489999999999998   4.919024293495611   0.000000000000000
+         95         1         1   0.000000000000000  14.910000000000000   4.919024293495611   0.000000000000000
+         96         1         1   0.000000000000000  15.619999999999999   6.148780366869514   0.000000000000000
+         97         1         1   0.000000000000000  17.039999999999999   6.148780366869514   0.000000000000000
+         98         1         1   0.000000000000000  17.750000000000000   4.919024293495611   0.000000000000000
+         99         1         1   0.000000000000000  19.169999999999998   4.919024293495611   0.000000000000000
+        100         1         1   0.000000000000000  19.879999999999999   6.148780366869514   0.000000000000000
+        101         1         1   0.000000000000000  21.299999999999997   6.148780366869514   0.000000000000000
+        102         1         1   0.000000000000000  22.009999999999998   4.919024293495611   0.000000000000000
+        103         1         1   0.000000000000000  23.429999999999996   4.919024293495611   0.000000000000000
+        104         1         1   0.000000000000000  24.139999999999997   6.148780366869514   0.000000000000000
+        105         1         1   0.000000000000000  25.559999999999999   6.148780366869514   0.000000000000000
+        106         1         1   0.000000000000000  26.270000000000000   4.919024293495611   0.000000000000000
+        107         1         1   0.000000000000000  27.689999999999998   4.919024293495611   0.000000000000000
+        108         1         1   0.000000000000000  28.399999999999999   6.148780366869514   0.000000000000000
+        109         1         1   0.000000000000000  29.820000000000000   6.148780366869514   0.000000000000000
+        110         1         1   0.000000000000000  30.530000000000001   4.919024293495611   0.000000000000000
+        111         1         1   0.000000000000000  31.949999999999999   4.919024293495611   0.000000000000000
+        112         1         1   0.000000000000000  32.659999999999997   6.148780366869514   0.000000000000000
+        113         1         1   0.000000000000000  34.079999999999998   6.148780366869514   0.000000000000000
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diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH-old.ILP b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH-old.ILP
deleted file mode 120000
index 9a3bc96225..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH-old.ILP
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../potentials/BNCH-old.ILP
\ No newline at end of file
diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH_300K.data b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH_300K.data
deleted file mode 100644
index be91806549..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH_300K.data
+++ /dev/null
@@ -1,2739 +0,0 @@
-LAMMPS data file via write_data, version 23 Oct 2017, timestep = 1000000
-
-1360 atoms
-2 atom types
-
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-0.0000000000000000e+00 4.1811706494712695e+01 ylo yhi
-0.0000000000000000e+00 1.0000000000000000e+02 zlo zhi
-
-Masses
-
-1 12.0107
-2 12.0107
-
-Atoms # full
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diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.airebo b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.airebo
deleted file mode 120000
index 5d070dd3a4..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.airebo
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../potentials/CH.airebo
\ No newline at end of file
diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene
deleted file mode 100644
index 8674917af2..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene
+++ /dev/null
@@ -1,61 +0,0 @@
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-# read lammps data file
-read_data       Bi_gr_AB_stack_2L_noH_300K.data
-mass            1 12.0107   # carbon mass (g/mole) | membrane
-mass            2 12.0107   # carbon mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1
-group adsorbate type 2
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo      NULL C  # chemical
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP   C    C  # long range
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair ilp/graphene/hbn
-variable  REBO     equal c_0
-variable  ILP      equal c_1
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.1 b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.1
deleted file mode 100644
index b93108646e..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.1
+++ /dev/null
@@ -1,137 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-# read lammps data file
-read_data       Bi_gr_AB_stack_2L_noH_300K.data
-  orthogonal box = (0 0 0) to (42.6 41.8117 100)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1360 atoms
-  reading velocities ...
-  1360 velocities
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 12.0107   # carbon mass (g/mole) | membrane
-mass            2 12.0107   # carbon mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1
-680 atoms in group membrane
-group adsorbate type 2
-680 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo      NULL C  # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP   C    C  # long range
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair ilp/graphene/hbn
-variable  REBO     equal c_0
-variable  ILP      equal c_1
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair rebo, perpetual, skip from (2)
-      attributes: full, newton on, ghost
-      pair build: skip/ghost
-      stencil: none
-      bin: none
-  (2) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes
-Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 
-       0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 
-     100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564 
-     200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465 
-     300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539 
-     400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113372 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709 
-     500 -5029.3985510533 -5046.0433160610 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534 
-     600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537 
-     700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274644 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955 
-     800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515 
-     900 -5029.3930414672 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839 
-    1000 -5029.3908907831 -5045.6437703691 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974 
-Loop time of 137.46 on 1 procs for 1000 steps with 1360 atoms
-
-Performance: 0.629 ns/day, 38.183 hours/ns, 7.275 timesteps/s
-95.1% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 137.33     | 137.33     | 137.33     |   0.0 | 99.90
-Bond    | 0.00071788 | 0.00071788 | 0.00071788 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.067907   | 0.067907   | 0.067907   |   0.0 |  0.05
-Output  | 0.0016029  | 0.0016029  | 0.0016029  |   0.0 |  0.00
-Modify  | 0.036542   | 0.036542   | 0.036542   |   0.0 |  0.03
-Other   |            | 0.02574    |            |       |  0.02
-
-Nlocal:    1360 ave 1360 max 1360 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    7964 ave 7964 max 7964 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  265206 ave 265206 max 265206 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 265206
-Ave neighs/atom = 195.004
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:02:17
diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.4 b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.4
deleted file mode 100644
index 6e28672714..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.4
+++ /dev/null
@@ -1,137 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-# read lammps data file
-read_data       Bi_gr_AB_stack_2L_noH_300K.data
-  orthogonal box = (0 0 0) to (42.6 41.8117 100)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  1360 atoms
-  reading velocities ...
-  1360 velocities
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 12.0107   # carbon mass (g/mole) | membrane
-mass            2 12.0107   # carbon mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1
-680 atoms in group membrane
-group adsorbate type 2
-680 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo      NULL C  # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP   C    C  # long range
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair ilp/graphene/hbn
-variable  REBO     equal c_0
-variable  ILP      equal c_1
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair rebo, perpetual, skip from (2)
-      attributes: full, newton on, ghost
-      pair build: skip/ghost
-      stencil: none
-      bin: none
-  (2) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 11.13 | 11.13 | 11.13 Mbytes
-Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 
-       0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 
-     100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564 
-     200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465 
-     300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539 
-     400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113371 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709 
-     500 -5029.3985510533 -5046.0433160611 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534 
-     600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537 
-     700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274643 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955 
-     800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515 
-     900 -5029.3930414671 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839 
-    1000 -5029.3908907831 -5045.6437703692 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974 
-Loop time of 36.0917 on 4 procs for 1000 steps with 1360 atoms
-
-Performance: 2.394 ns/day, 10.025 hours/ns, 27.707 timesteps/s
-97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 33.204     | 34.289     | 35.893     |  17.3 | 95.01
-Bond    | 0.00038719 | 0.00065947 | 0.00097609 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.1539     | 1.7595     | 2.8464     |  76.7 |  4.88
-Output  | 0.0013447  | 0.0014529  | 0.0016887  |   0.4 |  0.00
-Modify  | 0.010811   | 0.012037   | 0.013764   |   1.0 |  0.03
-Other   |            | 0.0287     |            |       |  0.08
-
-Nlocal:    340 ave 344 max 334 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-Nghost:    4628 ave 4634 max 4624 min
-Histogram: 1 0 1 0 1 0 0 0 0 1
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  66301.5 ave 67860 max 63963 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-
-Total # of neighbors = 265206
-Ave neighs/atom = 195.004
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:36
diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNC.tersoff b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNC.tersoff
deleted file mode 120000
index 0c35f80da1..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNC.tersoff
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../potentials/BNC.tersoff
\ No newline at end of file
diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH-old.ILP b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH-old.ILP
deleted file mode 120000
index 9a3bc96225..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH-old.ILP
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../potentials/BNCH-old.ILP
\ No newline at end of file
diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.airebo b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.airebo
deleted file mode 120000
index 5d070dd3a4..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.airebo
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../potentials/CH.airebo
\ No newline at end of file
diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN
deleted file mode 100644
index bad7b17fde..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN
+++ /dev/null
@@ -1,71 +0,0 @@
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       gr_hBN_Cstack_2L_noH.data
-mass            1 10.8110   # boron    mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | membrane
-mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-group adsorbate type 3
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo     NULL NULL C    # chemical
-pair_coeff  * * tersoff            BNC.tersoff   B    N    NULL # chemical
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP  B    N    C    # long range
-pair_coeff  1 1 coul/shield 0.70
-pair_coeff  1 2 coul/shield 0.69498201415576216335
-pair_coeff  2 2 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-velocity  all create 300.0 12345
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair tersoff
-compute   2 all pair ilp/graphene/hbn
-compute   3 all pair coul/shield
-variable  REBO     equal  c_0
-variable  Tersoff  equal  c_1
-variable  EILP     equal  c_2
-variable  Ecoul    equal  c_3
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.1 b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.1
deleted file mode 100644
index e5bce94ef4..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.1
+++ /dev/null
@@ -1,171 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       gr_hBN_Cstack_2L_noH.data
-  orthogonal box = (0 0 0) to (44.583 42.9 100)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1440 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 10.8110   # boron    mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | membrane
-mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-720 atoms in group membrane
-group adsorbate type 3
-720 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo     NULL NULL C    # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff  * * tersoff            BNC.tersoff   B    N    NULL # chemical
-Reading potential file BNC.tersoff with DATE: 2013-03-21
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP  B    N    C    # long range
-pair_coeff  1 1 coul/shield 0.70
-pair_coeff  1 2 coul/shield 0.69498201415576216335
-pair_coeff  2 2 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-velocity  all create 300.0 12345
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair tersoff
-compute   2 all pair ilp/graphene/hbn
-compute   3 all pair coul/shield
-variable  REBO     equal  c_0
-variable  Tersoff  equal  c_1
-variable  EILP     equal  c_2
-variable  Ecoul    equal  c_3
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  7 neighbor lists, perpetual/occasional/extra = 6 1 0
-  (1) pair rebo, perpetual, skip from (3)
-      attributes: full, newton on, ghost
-      pair build: skip/ghost
-      stencil: none
-      bin: none
-  (2) pair tersoff, perpetual, skip from (6)
-      attributes: full, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (3) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (4) pair coul/shield, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton/skip
-      stencil: none
-      bin: none
-  (5) compute group/group, occasional, copy from (7)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (6) neighbor class addition, perpetual, copy from (3)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (7) neighbor class addition, perpetual, half/full from (6)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 25.93 | 25.93 | 25.93 Mbytes
-Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 
-       0 -10708.4531746010 -10764.2547791975 55.8016045965 -66.8250335416 -5401.7347845703 -5322.2780762734 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755 
-     100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614 
-     200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321 
-     300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196 
-     400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799 
-     500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266 
-     600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507737 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624 
-     700 -10708.1867253590 -10736.6143955088 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688 
-     800 -10708.1733385055 -10736.0277775931 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693 
-     900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300 
-    1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943 
-Loop time of 149.449 on 1 procs for 1000 steps with 1440 atoms
-
-Performance: 0.578 ns/day, 41.514 hours/ns, 6.691 timesteps/s
-96.7% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 149.06     | 149.06     | 149.06     |   0.0 | 99.74
-Bond    | 0.00082946 | 0.00082946 | 0.00082946 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.068351   | 0.068351   | 0.068351   |   0.0 |  0.05
-Output  | 0.25935    | 0.25935    | 0.25935    |   0.0 |  0.17
-Modify  | 0.030915   | 0.030915   | 0.030915   |   0.0 |  0.02
-Other   |            | 0.02702    |            |       |  0.02
-
-Nlocal:    1440 ave 1440 max 1440 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    8180 ave 8180 max 8180 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    140400 ave 140400 max 140400 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  280800 ave 280800 max 280800 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 280800
-Ave neighs/atom = 195
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:02:29
diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.4 b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.4
deleted file mode 100644
index 86e93369ff..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.4
+++ /dev/null
@@ -1,171 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       gr_hBN_Cstack_2L_noH.data
-  orthogonal box = (0 0 0) to (44.583 42.9 100)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  1440 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 10.8110   # boron    mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | membrane
-mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-720 atoms in group membrane
-group adsorbate type 3
-720 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo     NULL NULL C    # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff  * * tersoff            BNC.tersoff   B    N    NULL # chemical
-Reading potential file BNC.tersoff with DATE: 2013-03-21
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP  B    N    C    # long range
-pair_coeff  1 1 coul/shield 0.70
-pair_coeff  1 2 coul/shield 0.69498201415576216335
-pair_coeff  2 2 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-velocity  all create 300.0 12345
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair tersoff
-compute   2 all pair ilp/graphene/hbn
-compute   3 all pair coul/shield
-variable  REBO     equal  c_0
-variable  Tersoff  equal  c_1
-variable  EILP     equal  c_2
-variable  Ecoul    equal  c_3
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  7 neighbor lists, perpetual/occasional/extra = 6 1 0
-  (1) pair rebo, perpetual, skip from (3)
-      attributes: full, newton on, ghost
-      pair build: skip/ghost
-      stencil: none
-      bin: none
-  (2) pair tersoff, perpetual, skip from (6)
-      attributes: full, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (3) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (4) pair coul/shield, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton/skip
-      stencil: none
-      bin: none
-  (5) compute group/group, occasional, copy from (7)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (6) neighbor class addition, perpetual, copy from (3)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (7) neighbor class addition, perpetual, half/full from (6)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 14.25 | 14.25 | 14.25 Mbytes
-Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 
-       0 -10708.4531746011 -10764.2547791976 55.8016045965 -66.8250335415 -5401.7347845703 -5322.2780762735 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755 
-     100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614 
-     200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321 
-     300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196 
-     400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799 
-     500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266 
-     600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507736 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624 
-     700 -10708.1867253590 -10736.6143955089 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688 
-     800 -10708.1733385055 -10736.0277775930 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693 
-     900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300 
-    1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943 
-Loop time of 39.6206 on 4 procs for 1000 steps with 1440 atoms
-
-Performance: 2.181 ns/day, 11.006 hours/ns, 25.239 timesteps/s
-98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 34.948     | 37.122     | 39.309     |  31.6 | 93.69
-Bond    | 0.00046444 | 0.0005914  | 0.00089121 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.20131    | 2.3895     | 4.565      | 124.7 |  6.03
-Output  | 0.069107   | 0.069157   | 0.069264   |   0.0 |  0.17
-Modify  | 0.010056   | 0.010403   | 0.010688   |   0.3 |  0.03
-Other   |            | 0.02875    |            |       |  0.07
-
-Nlocal:    360 ave 380 max 340 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    4716 ave 4736 max 4696 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    35100 ave 37050 max 33150 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-FullNghs:  70200 ave 74100 max 66300 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 280800
-Ave neighs/atom = 195
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:39
diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/gr_hBN_Cstack_2L_noH.data b/examples/USER/misc/ilp_graphene_hbn/gr_hBN_Cstack_2L_noH.data
similarity index 100%
rename from examples/USER/misc/ilp_graphene_hbn/gr-hBN/gr_hBN_Cstack_2L_noH.data
rename to examples/USER/misc/ilp_graphene_hbn/gr_hBN_Cstack_2L_noH.data
diff --git a/examples/USER/misc/ilp_graphene_hbn/hBN_AA_prime_stack_2L_noH.data b/examples/USER/misc/ilp_graphene_hbn/hBN_AA_prime_stack_2L_noH.data
new file mode 100644
index 0000000000..b965f74d30
--- /dev/null
+++ b/examples/USER/misc/ilp_graphene_hbn/hBN_AA_prime_stack_2L_noH.data
@@ -0,0 +1,1372 @@
+ Generate Bi-layer hBN
+
+   1360  atoms
+
+ 4 atom types
+
+    0.000000000000000  43.379999999999995 xlo xhi
+    0.000000000000000  42.577272951658138 ylo yhi
+    0.000000000000000 100.000000000000000 zlo zhi
+
+ Atoms
+
+          1         1         1   0.42000   0.000000000000000   1.252272733872298   0.000000000000000
+          2         1         2  -0.42000   0.723000000000000   0.000000000000000   0.000000000000000
+          3         1         1   0.42000   2.169000000000000   0.000000000000000   0.000000000000000
+          4         1         2  -0.42000   2.892000000000000   1.252272733872298   0.000000000000000
+          5         1         1   0.42000   4.338000000000000   1.252272733872298   0.000000000000000
+          6         1         2  -0.42000   5.061000000000000   0.000000000000000   0.000000000000000
+          7         1         1   0.42000   6.507000000000000   0.000000000000000   0.000000000000000
+          8         1         2  -0.42000   7.230000000000000   1.252272733872298   0.000000000000000
+          9         1         1   0.42000   8.676000000000000   1.252272733872298   0.000000000000000
+         10         1         2  -0.42000   9.399000000000001   0.000000000000000   0.000000000000000
+         11         1         1   0.42000  10.845000000000001   0.000000000000000   0.000000000000000
+         12         1         2  -0.42000  11.568000000000000   1.252272733872298   0.000000000000000
+         13         1         1   0.42000  13.013999999999999   1.252272733872298   0.000000000000000
+         14         1         2  -0.42000  13.737000000000000   0.000000000000000   0.000000000000000
+         15         1         1   0.42000  15.183000000000000   0.000000000000000   0.000000000000000
+         16         1         2  -0.42000  15.905999999999999   1.252272733872298   0.000000000000000
+         17         1         1   0.42000  17.352000000000000   1.252272733872298   0.000000000000000
+         18         1         2  -0.42000  18.074999999999999   0.000000000000000   0.000000000000000
+         19         1         1   0.42000  19.521000000000001   0.000000000000000   0.000000000000000
+         20         1         2  -0.42000  20.244000000000000   1.252272733872298   0.000000000000000
+         21         1         1   0.42000  21.690000000000001   1.252272733872298   0.000000000000000
+         22         1         2  -0.42000  22.413000000000000   0.000000000000000   0.000000000000000
+         23         1         1   0.42000  23.859000000000002   0.000000000000000   0.000000000000000
+         24         1         2  -0.42000  24.582000000000001   1.252272733872298   0.000000000000000
+         25         1         1   0.42000  26.027999999999999   1.252272733872298   0.000000000000000
+         26         1         2  -0.42000  26.750999999999998   0.000000000000000   0.000000000000000
+         27         1         1   0.42000  28.196999999999999   0.000000000000000   0.000000000000000
+         28         1         2  -0.42000  28.919999999999998   1.252272733872298   0.000000000000000
+         29         1         1   0.42000  30.366000000000000   1.252272733872298   0.000000000000000
+         30         1         2  -0.42000  31.088999999999999   0.000000000000000   0.000000000000000
+         31         1         1   0.42000  32.534999999999997   0.000000000000000   0.000000000000000
+         32         1         2  -0.42000  33.258000000000003   1.252272733872298   0.000000000000000
+         33         1         1   0.42000  34.704000000000001   1.252272733872298   0.000000000000000
+         34         1         2  -0.42000  35.427000000000000   0.000000000000000   0.000000000000000
+         35         1         1   0.42000  36.872999999999998   0.000000000000000   0.000000000000000
+         36         1         2  -0.42000  37.596000000000004   1.252272733872298   0.000000000000000
+         37         1         1   0.42000  39.042000000000002   1.252272733872298   0.000000000000000
+         38         1         2  -0.42000  39.765000000000001   0.000000000000000   0.000000000000000
+         39         1         1   0.42000  41.210999999999999   0.000000000000000   0.000000000000000
+         40         1         2  -0.42000  41.934000000000005   1.252272733872298   0.000000000000000
+         41         1         1   0.42000   0.000000000000000   3.756818201616894   0.000000000000000
+         42         1         2  -0.42000   0.723000000000000   2.504545467744596   0.000000000000000
+         43         1         1   0.42000   2.169000000000000   2.504545467744596   0.000000000000000
+         44         1         2  -0.42000   2.892000000000000   3.756818201616894   0.000000000000000
+         45         1         1   0.42000   4.338000000000000   3.756818201616894   0.000000000000000
+         46         1         2  -0.42000   5.061000000000000   2.504545467744596   0.000000000000000
+         47         1         1   0.42000   6.507000000000000   2.504545467744596   0.000000000000000
+         48         1         2  -0.42000   7.230000000000000   3.756818201616894   0.000000000000000
+         49         1         1   0.42000   8.676000000000000   3.756818201616894   0.000000000000000
+         50         1         2  -0.42000   9.399000000000001   2.504545467744596   0.000000000000000
+         51         1         1   0.42000  10.845000000000001   2.504545467744596   0.000000000000000
+         52         1         2  -0.42000  11.568000000000000   3.756818201616894   0.000000000000000
+         53         1         1   0.42000  13.013999999999999   3.756818201616894   0.000000000000000
+         54         1         2  -0.42000  13.737000000000000   2.504545467744596   0.000000000000000
+         55         1         1   0.42000  15.183000000000000   2.504545467744596   0.000000000000000
+         56         1         2  -0.42000  15.905999999999999   3.756818201616894   0.000000000000000
+         57         1         1   0.42000  17.352000000000000   3.756818201616894   0.000000000000000
+         58         1         2  -0.42000  18.074999999999999   2.504545467744596   0.000000000000000
+         59         1         1   0.42000  19.521000000000001   2.504545467744596   0.000000000000000
+         60         1         2  -0.42000  20.244000000000000   3.756818201616894   0.000000000000000
+         61         1         1   0.42000  21.690000000000001   3.756818201616894   0.000000000000000
+         62         1         2  -0.42000  22.413000000000000   2.504545467744596   0.000000000000000
+         63         1         1   0.42000  23.859000000000002   2.504545467744596   0.000000000000000
+         64         1         2  -0.42000  24.582000000000001   3.756818201616894   0.000000000000000
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+       1204         2         3   0.42000   2.892000000000000  33.811363814552045   3.330000000000000
+       1205         2         4  -0.42000   4.338000000000000  33.811363814552045   3.330000000000000
+       1206         2         3   0.42000   5.061000000000000  32.559091080679750   3.330000000000000
+       1207         2         4  -0.42000   6.507000000000000  32.559091080679750   3.330000000000000
+       1208         2         3   0.42000   7.230000000000000  33.811363814552045   3.330000000000000
+       1209         2         4  -0.42000   8.676000000000000  33.811363814552045   3.330000000000000
+       1210         2         3   0.42000   9.399000000000001  32.559091080679750   3.330000000000000
+       1211         2         4  -0.42000  10.845000000000001  32.559091080679750   3.330000000000000
+       1212         2         3   0.42000  11.568000000000000  33.811363814552045   3.330000000000000
+       1213         2         4  -0.42000  13.013999999999999  33.811363814552045   3.330000000000000
+       1214         2         3   0.42000  13.737000000000000  32.559091080679750   3.330000000000000
+       1215         2         4  -0.42000  15.183000000000000  32.559091080679750   3.330000000000000
+       1216         2         3   0.42000  15.905999999999999  33.811363814552045   3.330000000000000
+       1217         2         4  -0.42000  17.352000000000000  33.811363814552045   3.330000000000000
+       1218         2         3   0.42000  18.074999999999999  32.559091080679750   3.330000000000000
+       1219         2         4  -0.42000  19.521000000000001  32.559091080679750   3.330000000000000
+       1220         2         3   0.42000  20.244000000000000  33.811363814552045   3.330000000000000
+       1221         2         4  -0.42000  21.690000000000001  33.811363814552045   3.330000000000000
+       1222         2         3   0.42000  22.413000000000000  32.559091080679750   3.330000000000000
+       1223         2         4  -0.42000  23.859000000000002  32.559091080679750   3.330000000000000
+       1224         2         3   0.42000  24.582000000000001  33.811363814552045   3.330000000000000
+       1225         2         4  -0.42000  26.027999999999999  33.811363814552045   3.330000000000000
+       1226         2         3   0.42000  26.750999999999998  32.559091080679750   3.330000000000000
+       1227         2         4  -0.42000  28.196999999999999  32.559091080679750   3.330000000000000
+       1228         2         3   0.42000  28.919999999999998  33.811363814552045   3.330000000000000
+       1229         2         4  -0.42000  30.366000000000000  33.811363814552045   3.330000000000000
+       1230         2         3   0.42000  31.088999999999999  32.559091080679750   3.330000000000000
+       1231         2         4  -0.42000  32.534999999999997  32.559091080679750   3.330000000000000
+       1232         2         3   0.42000  33.258000000000003  33.811363814552045   3.330000000000000
+       1233         2         4  -0.42000  34.704000000000001  33.811363814552045   3.330000000000000
+       1234         2         3   0.42000  35.427000000000000  32.559091080679750   3.330000000000000
+       1235         2         4  -0.42000  36.872999999999998  32.559091080679750   3.330000000000000
+       1236         2         3   0.42000  37.596000000000004  33.811363814552045   3.330000000000000
+       1237         2         4  -0.42000  39.042000000000002  33.811363814552045   3.330000000000000
+       1238         2         3   0.42000  39.765000000000001  32.559091080679750   3.330000000000000
+       1239         2         4  -0.42000  41.210999999999999  32.559091080679750   3.330000000000000
+       1240         2         3   0.42000  41.934000000000005  33.811363814552045   3.330000000000000
+       1241         2         4  -0.42000   0.000000000000000  36.315909282296644   3.330000000000000
+       1242         2         3   0.42000   0.723000000000000  35.063636548424348   3.330000000000000
+       1243         2         4  -0.42000   2.169000000000000  35.063636548424348   3.330000000000000
+       1244         2         3   0.42000   2.892000000000000  36.315909282296644   3.330000000000000
+       1245         2         4  -0.42000   4.338000000000000  36.315909282296644   3.330000000000000
+       1246         2         3   0.42000   5.061000000000000  35.063636548424348   3.330000000000000
+       1247         2         4  -0.42000   6.507000000000000  35.063636548424348   3.330000000000000
+       1248         2         3   0.42000   7.230000000000000  36.315909282296644   3.330000000000000
+       1249         2         4  -0.42000   8.676000000000000  36.315909282296644   3.330000000000000
+       1250         2         3   0.42000   9.399000000000001  35.063636548424348   3.330000000000000
+       1251         2         4  -0.42000  10.845000000000001  35.063636548424348   3.330000000000000
+       1252         2         3   0.42000  11.568000000000000  36.315909282296644   3.330000000000000
+       1253         2         4  -0.42000  13.013999999999999  36.315909282296644   3.330000000000000
+       1254         2         3   0.42000  13.737000000000000  35.063636548424348   3.330000000000000
+       1255         2         4  -0.42000  15.183000000000000  35.063636548424348   3.330000000000000
+       1256         2         3   0.42000  15.905999999999999  36.315909282296644   3.330000000000000
+       1257         2         4  -0.42000  17.352000000000000  36.315909282296644   3.330000000000000
+       1258         2         3   0.42000  18.074999999999999  35.063636548424348   3.330000000000000
+       1259         2         4  -0.42000  19.521000000000001  35.063636548424348   3.330000000000000
+       1260         2         3   0.42000  20.244000000000000  36.315909282296644   3.330000000000000
+       1261         2         4  -0.42000  21.690000000000001  36.315909282296644   3.330000000000000
+       1262         2         3   0.42000  22.413000000000000  35.063636548424348   3.330000000000000
+       1263         2         4  -0.42000  23.859000000000002  35.063636548424348   3.330000000000000
+       1264         2         3   0.42000  24.582000000000001  36.315909282296644   3.330000000000000
+       1265         2         4  -0.42000  26.027999999999999  36.315909282296644   3.330000000000000
+       1266         2         3   0.42000  26.750999999999998  35.063636548424348   3.330000000000000
+       1267         2         4  -0.42000  28.196999999999999  35.063636548424348   3.330000000000000
+       1268         2         3   0.42000  28.919999999999998  36.315909282296644   3.330000000000000
+       1269         2         4  -0.42000  30.366000000000000  36.315909282296644   3.330000000000000
+       1270         2         3   0.42000  31.088999999999999  35.063636548424348   3.330000000000000
+       1271         2         4  -0.42000  32.534999999999997  35.063636548424348   3.330000000000000
+       1272         2         3   0.42000  33.258000000000003  36.315909282296644   3.330000000000000
+       1273         2         4  -0.42000  34.704000000000001  36.315909282296644   3.330000000000000
+       1274         2         3   0.42000  35.427000000000000  35.063636548424348   3.330000000000000
+       1275         2         4  -0.42000  36.872999999999998  35.063636548424348   3.330000000000000
+       1276         2         3   0.42000  37.596000000000004  36.315909282296644   3.330000000000000
+       1277         2         4  -0.42000  39.042000000000002  36.315909282296644   3.330000000000000
+       1278         2         3   0.42000  39.765000000000001  35.063636548424348   3.330000000000000
+       1279         2         4  -0.42000  41.210999999999999  35.063636548424348   3.330000000000000
+       1280         2         3   0.42000  41.934000000000005  36.315909282296644   3.330000000000000
+       1281         2         4  -0.42000   0.000000000000000  38.820454750041236   3.330000000000000
+       1282         2         3   0.42000   0.723000000000000  37.568182016168940   3.330000000000000
+       1283         2         4  -0.42000   2.169000000000000  37.568182016168940   3.330000000000000
+       1284         2         3   0.42000   2.892000000000000  38.820454750041236   3.330000000000000
+       1285         2         4  -0.42000   4.338000000000000  38.820454750041236   3.330000000000000
+       1286         2         3   0.42000   5.061000000000000  37.568182016168940   3.330000000000000
+       1287         2         4  -0.42000   6.507000000000000  37.568182016168940   3.330000000000000
+       1288         2         3   0.42000   7.230000000000000  38.820454750041236   3.330000000000000
+       1289         2         4  -0.42000   8.676000000000000  38.820454750041236   3.330000000000000
+       1290         2         3   0.42000   9.399000000000001  37.568182016168940   3.330000000000000
+       1291         2         4  -0.42000  10.845000000000001  37.568182016168940   3.330000000000000
+       1292         2         3   0.42000  11.568000000000000  38.820454750041236   3.330000000000000
+       1293         2         4  -0.42000  13.013999999999999  38.820454750041236   3.330000000000000
+       1294         2         3   0.42000  13.737000000000000  37.568182016168940   3.330000000000000
+       1295         2         4  -0.42000  15.183000000000000  37.568182016168940   3.330000000000000
+       1296         2         3   0.42000  15.905999999999999  38.820454750041236   3.330000000000000
+       1297         2         4  -0.42000  17.352000000000000  38.820454750041236   3.330000000000000
+       1298         2         3   0.42000  18.074999999999999  37.568182016168940   3.330000000000000
+       1299         2         4  -0.42000  19.521000000000001  37.568182016168940   3.330000000000000
+       1300         2         3   0.42000  20.244000000000000  38.820454750041236   3.330000000000000
+       1301         2         4  -0.42000  21.690000000000001  38.820454750041236   3.330000000000000
+       1302         2         3   0.42000  22.413000000000000  37.568182016168940   3.330000000000000
+       1303         2         4  -0.42000  23.859000000000002  37.568182016168940   3.330000000000000
+       1304         2         3   0.42000  24.582000000000001  38.820454750041236   3.330000000000000
+       1305         2         4  -0.42000  26.027999999999999  38.820454750041236   3.330000000000000
+       1306         2         3   0.42000  26.750999999999998  37.568182016168940   3.330000000000000
+       1307         2         4  -0.42000  28.196999999999999  37.568182016168940   3.330000000000000
+       1308         2         3   0.42000  28.919999999999998  38.820454750041236   3.330000000000000
+       1309         2         4  -0.42000  30.366000000000000  38.820454750041236   3.330000000000000
+       1310         2         3   0.42000  31.088999999999999  37.568182016168940   3.330000000000000
+       1311         2         4  -0.42000  32.534999999999997  37.568182016168940   3.330000000000000
+       1312         2         3   0.42000  33.258000000000003  38.820454750041236   3.330000000000000
+       1313         2         4  -0.42000  34.704000000000001  38.820454750041236   3.330000000000000
+       1314         2         3   0.42000  35.427000000000000  37.568182016168940   3.330000000000000
+       1315         2         4  -0.42000  36.872999999999998  37.568182016168940   3.330000000000000
+       1316         2         3   0.42000  37.596000000000004  38.820454750041236   3.330000000000000
+       1317         2         4  -0.42000  39.042000000000002  38.820454750041236   3.330000000000000
+       1318         2         3   0.42000  39.765000000000001  37.568182016168940   3.330000000000000
+       1319         2         4  -0.42000  41.210999999999999  37.568182016168940   3.330000000000000
+       1320         2         3   0.42000  41.934000000000005  38.820454750041236   3.330000000000000
+       1321         2         4  -0.42000   0.000000000000000  41.325000217785835   3.330000000000000
+       1322         2         3   0.42000   0.723000000000000  40.072727483913539   3.330000000000000
+       1323         2         4  -0.42000   2.169000000000000  40.072727483913539   3.330000000000000
+       1324         2         3   0.42000   2.892000000000000  41.325000217785835   3.330000000000000
+       1325         2         4  -0.42000   4.338000000000000  41.325000217785835   3.330000000000000
+       1326         2         3   0.42000   5.061000000000000  40.072727483913539   3.330000000000000
+       1327         2         4  -0.42000   6.507000000000000  40.072727483913539   3.330000000000000
+       1328         2         3   0.42000   7.230000000000000  41.325000217785835   3.330000000000000
+       1329         2         4  -0.42000   8.676000000000000  41.325000217785835   3.330000000000000
+       1330         2         3   0.42000   9.399000000000001  40.072727483913539   3.330000000000000
+       1331         2         4  -0.42000  10.845000000000001  40.072727483913539   3.330000000000000
+       1332         2         3   0.42000  11.568000000000000  41.325000217785835   3.330000000000000
+       1333         2         4  -0.42000  13.013999999999999  41.325000217785835   3.330000000000000
+       1334         2         3   0.42000  13.737000000000000  40.072727483913539   3.330000000000000
+       1335         2         4  -0.42000  15.183000000000000  40.072727483913539   3.330000000000000
+       1336         2         3   0.42000  15.905999999999999  41.325000217785835   3.330000000000000
+       1337         2         4  -0.42000  17.352000000000000  41.325000217785835   3.330000000000000
+       1338         2         3   0.42000  18.074999999999999  40.072727483913539   3.330000000000000
+       1339         2         4  -0.42000  19.521000000000001  40.072727483913539   3.330000000000000
+       1340         2         3   0.42000  20.244000000000000  41.325000217785835   3.330000000000000
+       1341         2         4  -0.42000  21.690000000000001  41.325000217785835   3.330000000000000
+       1342         2         3   0.42000  22.413000000000000  40.072727483913539   3.330000000000000
+       1343         2         4  -0.42000  23.859000000000002  40.072727483913539   3.330000000000000
+       1344         2         3   0.42000  24.582000000000001  41.325000217785835   3.330000000000000
+       1345         2         4  -0.42000  26.027999999999999  41.325000217785835   3.330000000000000
+       1346         2         3   0.42000  26.750999999999998  40.072727483913539   3.330000000000000
+       1347         2         4  -0.42000  28.196999999999999  40.072727483913539   3.330000000000000
+       1348         2         3   0.42000  28.919999999999998  41.325000217785835   3.330000000000000
+       1349         2         4  -0.42000  30.366000000000000  41.325000217785835   3.330000000000000
+       1350         2         3   0.42000  31.088999999999999  40.072727483913539   3.330000000000000
+       1351         2         4  -0.42000  32.534999999999997  40.072727483913539   3.330000000000000
+       1352         2         3   0.42000  33.258000000000003  41.325000217785835   3.330000000000000
+       1353         2         4  -0.42000  34.704000000000001  41.325000217785835   3.330000000000000
+       1354         2         3   0.42000  35.427000000000000  40.072727483913539   3.330000000000000
+       1355         2         4  -0.42000  36.872999999999998  40.072727483913539   3.330000000000000
+       1356         2         3   0.42000  37.596000000000004  41.325000217785835   3.330000000000000
+       1357         2         4  -0.42000  39.042000000000002  41.325000217785835   3.330000000000000
+       1358         2         3   0.42000  39.765000000000001  40.072727483913539   3.330000000000000
+       1359         2         4  -0.42000  41.210999999999999  40.072727483913539   3.330000000000000
+       1360         2         3   0.42000  41.934000000000005  41.325000217785835   3.330000000000000
diff --git a/examples/USER/misc/ilp_graphene_hbn/in.bilayer-graphene b/examples/USER/misc/ilp_graphene_hbn/in.bilayer-graphene
new file mode 100644
index 0000000000..0ef2787744
--- /dev/null
+++ b/examples/USER/misc/ilp_graphene_hbn/in.bilayer-graphene
@@ -0,0 +1,51 @@
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+
+read_data       Bi_gr_AB_stack_2L_noH.data
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Separate atom groups
+group		layer1 molecule 1
+group		layer2 molecule 2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo   C  C  # chemical
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP  C  C  # long range
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep	0.001
+velocity	all create 300.0 12345
+
+compute   	0 all pair rebo
+compute  	1 all pair ilp/graphene/hbn
+variable  	REBO  equal c_0     # REBO energy
+variable  	ILP   equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+fix       	thermostat all nve
+run 	  	1000
diff --git a/examples/USER/misc/ilp_graphene_hbn/in.bilayer-hBN b/examples/USER/misc/ilp_graphene_hbn/in.bilayer-hBN
new file mode 100644
index 0000000000..1cf982d8dc
--- /dev/null
+++ b/examples/USER/misc/ilp_graphene_hbn/in.bilayer-hBN
@@ -0,0 +1,56 @@
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AA_prime_stack_2L_noH.data
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group 		layer1 molecule 1
+group 		layer2 molecule 2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff B N B N  # chemical
+pair_coeff  * * ilp/graphene/hbn BNCH.ILP    B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair tersoff
+compute   	1 all pair coul/shield ecoul
+compute   	2 all pair ilp/graphene/hbn
+variable  	Tersoff  equal c_0     # Tersoff energy
+variable  	Ecoul    equal c_1     # Coulomb energy
+variable  	EILP     equal c_2     # total interlayer energy
+variable  	Evdw     equal c_2[1]  # attractive energy
+variable 	Erep     equal c_2[2]  # repulsive  energy
+
+############# Output ###############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+run 		1000
diff --git a/examples/USER/misc/ilp_graphene_hbn/in.grhBN b/examples/USER/misc/ilp_graphene_hbn/in.grhBN
new file mode 100644
index 0000000000..46c42e0d6d
--- /dev/null
+++ b/examples/USER/misc/ilp_graphene_hbn/in.grhBN
@@ -0,0 +1,56 @@
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       gr_hBN_Cstack_2L_noH.data
+mass            1 10.8110   # boron    mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | membrane
+mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
+# Separate atom groups
+group 		hBN molecule 1
+group 		gr  molecule 2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo     NULL NULL C    # chemical
+pair_coeff  * * tersoff            BNC.tersoff B    N    NULL # chemical
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP    B    N    C    # long range
+pair_coeff  1 1 coul/shield 0.70
+pair_coeff  1 2 coul/shield 0.69498201415576216335
+pair_coeff  2 2 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair rebo
+compute   	1 all pair tersoff
+compute   	2 all pair ilp/graphene/hbn
+compute   	3 all pair coul/shield
+variable  	REBO     equal  c_0
+variable  	Tersoff  equal  c_1
+variable  	EILP     equal  c_2     # total interlayer energy
+variable  	Evdw     equal  c_2[1]  # attractive energy
+variable 	Erep     equal  c_2[2]  # repulsive  energy
+variable  	Ecoul    equal  c_3
+
+############# Output ##############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
+
+###### Run molecular dynamics ######
+run 		1000
diff --git a/examples/USER/misc/ilp_graphene_hbn/in.ilp_graphene_hbn b/examples/USER/misc/ilp_graphene_hbn/in.ilp_graphene_hbn
index da813b3d10..9b122e194e 100644
--- a/examples/USER/misc/ilp_graphene_hbn/in.ilp_graphene_hbn
+++ b/examples/USER/misc/ilp_graphene_hbn/in.ilp_graphene_hbn
@@ -32,14 +32,6 @@ neigh_modify    every 1
 neigh_modify    delay 0
 neigh_modify    check yes
 
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
 #### Simulation settings ####
 timestep  0.001
 #velocity  adsorbate create 300.0 12345
@@ -51,19 +43,16 @@ compute   1 all pair coul/shield ecoul
 compute   2 all pair ilp/graphene/hbn
 variable  Tersoff  equal c_0
 variable  Ecoul    equal c_1
-variable  EILP     equal c_2
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
+variable  ILP      equal c_2
+variable  Evdw     equal c_2[1]
+variable  Erep     equal c_2[2]
 
 ############################
 
 # Output
 thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn #ignore
+thermo_style    custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
+thermo_modify   lost warn #ignore
 
 #dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
 #dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
diff --git a/examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.1 b/examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.1
deleted file mode 100644
index fc10948f9a..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.1
+++ /dev/null
@@ -1,168 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       hBN_AB_stack_2L_noH_equi_300K.data
-  orthogonal box = (0 0 0) to (43.38 42.5773 100)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1360 atoms
-  reading velocities ...
-  1360 velocities
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 10.8110   # boron mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
-mass            3 10.8110   # boron mass (g/mole) | membrane
-mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-680 atoms in group membrane
-group adsorbate type 3 4
-680 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
-####################################################################
-pair_coeff  * * tersoff          BNC.tersoff   NULL NULL B N  # chemical
-Reading potential file BNC.tersoff with DATE: 2013-03-21
-pair_coeff  * * ilp/graphene/hbn BNCH-old.ILP  B N B N  # long range
-pair_coeff  1 3 coul/shield 0.70
-pair_coeff  1 4 coul/shield 0.69498201415576216335
-pair_coeff  2 3 coul/shield 0.69498201415576216335
-pair_coeff  2 4 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair tersoff
-compute   1 all pair coul/shield ecoul
-compute   2 all pair ilp/graphene/hbn
-variable  Tersoff  equal c_0
-variable  Ecoul    equal c_1
-variable  EILP     equal c_2
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn #ignore
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  6 neighbor lists, perpetual/occasional/extra = 5 1 0
-  (1) pair tersoff, perpetual, skip from (5)
-      attributes: full, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (2) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (3) pair coul/shield, perpetual, skip from (6)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (4) compute group/group, occasional, copy from (6)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (5) neighbor class addition, perpetual, copy from (2)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (6) neighbor class addition, perpetual, half/full from (5)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 57.85 | 57.85 | 57.85 Mbytes
-Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3] 
-       0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801 
-     100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275 
-     200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807 
-     300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614 
-     400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122 
-     500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319 
-     600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794 
-     700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989 
-     800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553 
-     900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606 
-    1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557 
-Loop time of 202.063 on 1 procs for 1000 steps with 1360 atoms
-
-Performance: 0.428 ns/day, 56.129 hours/ns, 4.949 timesteps/s
-91.0% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 201.4      | 201.4      | 201.4      |   0.0 | 99.67
-Bond    | 0.00092697 | 0.00092697 | 0.00092697 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.086005   | 0.086005   | 0.086005   |   0.0 |  0.04
-Output  | 0.50438    | 0.50438    | 0.50438    |   0.0 |  0.25
-Modify  | 0.038846   | 0.038846   | 0.038846   |   0.0 |  0.02
-Other   |            | 0.03093    |            |       |  0.02
-
-Nlocal:    1360 ave 1360 max 1360 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    7840 ave 7840 max 7840 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    249628 ave 249628 max 249628 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  253390 ave 253390 max 253390 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 253390
-Ave neighs/atom = 186.316
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:03:22
diff --git a/examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.4 b/examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.4
deleted file mode 100644
index 5cd3518918..0000000000
--- a/examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.4
+++ /dev/null
@@ -1,168 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       hBN_AB_stack_2L_noH_equi_300K.data
-  orthogonal box = (0 0 0) to (43.38 42.5773 100)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  1360 atoms
-  reading velocities ...
-  1360 velocities
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 10.8110   # boron mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
-mass            3 10.8110   # boron mass (g/mole) | membrane
-mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-680 atoms in group membrane
-group adsorbate type 3 4
-680 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
-####################################################################
-pair_coeff  * * tersoff          BNC.tersoff   NULL NULL B N  # chemical
-Reading potential file BNC.tersoff with DATE: 2013-03-21
-pair_coeff  * * ilp/graphene/hbn BNCH-old.ILP  B N B N  # long range
-pair_coeff  1 3 coul/shield 0.70
-pair_coeff  1 4 coul/shield 0.69498201415576216335
-pair_coeff  2 3 coul/shield 0.69498201415576216335
-pair_coeff  2 4 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair tersoff
-compute   1 all pair coul/shield ecoul
-compute   2 all pair ilp/graphene/hbn
-variable  Tersoff  equal c_0
-variable  Ecoul    equal c_1
-variable  EILP     equal c_2
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn #ignore
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  6 neighbor lists, perpetual/occasional/extra = 5 1 0
-  (1) pair tersoff, perpetual, skip from (5)
-      attributes: full, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (2) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (3) pair coul/shield, perpetual, skip from (6)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (4) compute group/group, occasional, copy from (6)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (5) neighbor class addition, perpetual, copy from (2)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (6) neighbor class addition, perpetual, half/full from (5)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 30.63 | 30.63 | 30.64 Mbytes
-Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3] 
-       0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801 
-     100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275 
-     200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807 
-     300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614 
-     400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122 
-     500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319 
-     600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794 
-     700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989 
-     800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553 
-     900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606 
-    1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557 
-Loop time of 53.3155 on 4 procs for 1000 steps with 1360 atoms
-
-Performance: 1.621 ns/day, 14.810 hours/ns, 18.756 timesteps/s
-97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 49.475     | 50.978     | 52.988     |  18.0 | 95.62
-Bond    | 0.00045061 | 0.00066602 | 0.00086665 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.16491    | 2.1759     | 3.679      |  87.0 |  4.08
-Output  | 0.11871    | 0.11882    | 0.11911    |   0.0 |  0.22
-Modify  | 0.012956   | 0.013504   | 0.01387    |   0.3 |  0.03
-Other   |            | 0.02828    |            |       |  0.05
-
-Nlocal:    340 ave 346 max 336 min
-Histogram: 1 0 1 0 1 0 0 0 0 1
-Nghost:    4537.5 ave 4540 max 4534 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-Neighs:    62407 ave 62413 max 62402 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-FullNghs:  63347.5 ave 65585 max 61866 min
-Histogram: 1 1 0 1 0 0 0 0 0 1
-
-Total # of neighbors = 253926
-Ave neighs/atom = 186.71
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:53
diff --git a/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.1 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.1
new file mode 100644
index 0000000000..df3a7b70ab
--- /dev/null
+++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.1
@@ -0,0 +1,127 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+
+read_data       Bi_gr_AB_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (42.6 41.8117 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000290871 secs
+  read_data CPU = 0.00159073 secs
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Separate atom groups
+group		layer1 molecule 1
+680 atoms in group layer1
+group		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo   C  C  # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP  C  C  # long range
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep	0.001
+velocity	all create 300.0 12345
+
+compute   	0 all pair rebo
+compute  	1 all pair ilp/graphene/hbn
+variable  	REBO  equal c_0     # REBO energy
+variable  	ILP   equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+fix       	thermostat all nve
+run 	  	1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair ilp/graphene/hbn, perpetual, copy from (1)
+      attributes: full, newton on, ghost
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes
+Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp 
+       0   -10037.285   -10089.985    52.699361   -10057.189   -32.795185    43.640104   -76.435288          300 
+     100   -10037.034   -10064.765     27.73131   -10032.181    -32.58421    34.730868   -67.315078    157.86516 
+     200   -10036.963   -10061.144     24.18111   -10028.856   -32.288132    28.179936   -60.468068    137.65505 
+     300   -10037.003     -10063.5    26.496726   -10030.823   -32.677105    34.923849   -67.600954    150.83708 
+     400   -10037.032   -10064.389    27.356526   -10031.853   -32.535415    44.242347   -76.777762    155.73164 
+     500   -10037.023   -10064.114    27.090279   -10031.431   -32.682418    37.229232    -69.91165    154.21598 
+     600   -10037.003   -10063.657    26.653718   -10031.327   -32.329664    28.509073   -60.838737    151.73078 
+     700   -10037.004    -10063.35    26.345697   -10030.801   -32.549231    32.564686   -65.113917    149.97732 
+     800   -10037.025   -10064.219    27.194765   -10031.766   -32.453653    43.381557    -75.83521    154.81078 
+     900   -10037.028   -10064.668    27.639127   -10032.167   -32.500121     39.99345   -72.493571    157.34039 
+    1000   -10037.003   -10063.662    26.658825   -10031.337   -32.325053    29.573578   -61.898631    151.75986 
+Loop time of 149.887 on 1 procs for 1000 steps with 1360 atoms
+
+Performance: 0.576 ns/day, 41.635 hours/ns, 6.672 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 149.75     | 149.75     | 149.75     |   0.0 | 99.91
+Bond    | 0.00024772 | 0.00024772 | 0.00024772 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.086328   | 0.086328   | 0.086328   |   0.0 |  0.06
+Output  | 0.00036383 | 0.00036383 | 0.00036383 |   0.0 |  0.00
+Modify  | 0.028636   | 0.028636   | 0.028636   |   0.0 |  0.02
+Other   |            | 0.01708    |            |       |  0.01
+
+Nlocal:    1360 ave 1360 max 1360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7964 ave 7964 max 7964 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  1.037e+06 ave 1.037e+06 max 1.037e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037000
+Ave neighs/atom = 762.5
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:02:30
diff --git a/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.4 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.4
new file mode 100644
index 0000000000..9ecc05ce6d
--- /dev/null
+++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.4
@@ -0,0 +1,127 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+
+read_data       Bi_gr_AB_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (42.6 41.8117 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000157118 secs
+  read_data CPU = 0.00145698 secs
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Separate atom groups
+group		layer1 molecule 1
+680 atoms in group layer1
+group		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo   C  C  # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP  C  C  # long range
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep	0.001
+velocity	all create 300.0 12345
+
+compute   	0 all pair rebo
+compute  	1 all pair ilp/graphene/hbn
+variable  	REBO  equal c_0     # REBO energy
+variable  	ILP   equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+fix       	thermostat all nve
+run 	  	1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair ilp/graphene/hbn, perpetual, copy from (1)
+      attributes: full, newton on, ghost
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.879 | 9.879 | 9.879 Mbytes
+Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp 
+       0   -10037.285   -10089.985    52.699361   -10057.189   -32.795185    43.640104   -76.435288          300 
+     100   -10037.034   -10064.765     27.73131   -10032.181    -32.58421    34.730868   -67.315078    157.86516 
+     200   -10036.963   -10061.144     24.18111   -10028.856   -32.288132    28.179936   -60.468068    137.65505 
+     300   -10037.003     -10063.5    26.496726   -10030.823   -32.677105    34.923849   -67.600954    150.83708 
+     400   -10037.032   -10064.389    27.356526   -10031.853   -32.535415    44.242347   -76.777762    155.73164 
+     500   -10037.023   -10064.114    27.090279   -10031.431   -32.682418    37.229232    -69.91165    154.21598 
+     600   -10037.003   -10063.657    26.653718   -10031.327   -32.329664    28.509073   -60.838737    151.73078 
+     700   -10037.004    -10063.35    26.345697   -10030.801   -32.549231    32.564686   -65.113917    149.97732 
+     800   -10037.025   -10064.219    27.194765   -10031.766   -32.453653    43.381557    -75.83521    154.81078 
+     900   -10037.028   -10064.668    27.639127   -10032.167   -32.500121     39.99345   -72.493571    157.34039 
+    1000   -10037.003   -10063.662    26.658825   -10031.337   -32.325053    29.573578   -61.898631    151.75986 
+Loop time of 44.6551 on 4 procs for 1000 steps with 1360 atoms
+
+Performance: 1.935 ns/day, 12.404 hours/ns, 22.394 timesteps/s
+93.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 40.304     | 41.221     | 41.998     |   9.5 | 92.31
+Bond    | 0.00027633 | 0.00029379 | 0.00031424 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 2.5678     | 3.3334     | 4.2403     |  32.9 |  7.46
+Output  | 0.0051446  | 0.0054518  | 0.0059683  |   0.4 |  0.01
+Modify  | 0.0088317  | 0.009002   | 0.0090654  |   0.1 |  0.02
+Other   |            | 0.08586    |            |       |  0.19
+
+Nlocal:    340 ave 340 max 340 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    4628 ave 4628 max 4628 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  259250 ave 259250 max 259250 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037000
+Ave neighs/atom = 762.5
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:44
diff --git a/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.1 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.1
new file mode 100644
index 0000000000..c5c6e94f15
--- /dev/null
+++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.1
@@ -0,0 +1,142 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AA_prime_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (43.38 42.5773 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000375509 secs
+  read_data CPU = 0.00181293 secs
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group 		layer1 molecule 1
+680 atoms in group layer1
+group 		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff B N B N  # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn BNCH.ILP    B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair tersoff
+compute   	1 all pair coul/shield ecoul
+compute   	2 all pair ilp/graphene/hbn
+variable  	Tersoff  equal c_0     # Tersoff energy
+variable  	Ecoul    equal c_1     # Coulomb energy
+variable  	EILP     equal c_2     # total interlayer energy
+variable  	Evdw     equal c_2[1]  # attractive energy
+variable 	Erep     equal c_2[2]  # repulsive  energy
+
+############# Output ###############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+run 		1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  4 neighbor lists, perpetual/occasional/extra = 4 0 0
+  (1) pair tersoff, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (3) pair coul/shield, perpetual, skip from (4)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) neighbor class addition, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 35.9 | 35.9 | 35.9 Mbytes
+Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp 
+       0   -10193.138   -10245.837    52.699361   -77.557069    -10208.73   -36.776483    40.780586   -77.557069  -0.33075117          300 
+     100   -10192.814   -10215.193     22.37957   -80.997619   -10177.878   -36.967736    44.029884   -80.997619  -0.34809915    127.39947 
+     200   -10192.922   -10221.807    28.884855   -86.370319   -10184.251   -37.168986    49.201334   -86.370319  -0.38644764    164.43191 
+     300   -10192.878   -10219.029    26.151464   -83.063924   -10182.349    -36.30412    46.759804   -83.063924  -0.37660157    148.87162 
+     400   -10192.892   -10218.834    25.942229   -78.394242   -10181.398   -37.110968    41.283274   -78.394242  -0.32494569    147.68051 
+     500   -10192.909   -10221.331    28.422213   -81.768531    -10184.03   -36.946226    44.822304   -81.768531  -0.35489965    161.79824 
+     600   -10192.886   -10219.371     26.48495   -86.278335   -10182.669    -36.29515    49.983185   -86.278335  -0.40636253    150.77004 
+     700   -10192.902    -10220.95    28.048108    -82.28873   -10183.208    -37.39374     44.89499    -82.28873  -0.34777958    159.66859 
+     800    -10192.88    -10218.51    25.630186   -78.011019   -10181.427   -36.754209    41.256811   -78.011019  -0.32904942    145.90415 
+     900   -10192.894    -10220.56    27.665437   -82.474379   -10183.801   -36.381157    46.093222   -82.474379  -0.37703328    157.49017 
+    1000   -10192.897    -10219.01     26.11313   -87.125683   -10181.252   -37.361898    49.763785   -87.125683  -0.39607952    148.65339 
+Loop time of 211.527 on 1 procs for 1000 steps with 1360 atoms
+
+Performance: 0.408 ns/day, 58.757 hours/ns, 4.728 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 211.4      | 211.4      | 211.4      |   0.0 | 99.94
+Bond    | 0.00018859 | 0.00018859 | 0.00018859 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.082034   | 0.082034   | 0.082034   |   0.0 |  0.04
+Output  | 0.00037289 | 0.00037289 | 0.00037289 |   0.0 |  0.00
+Modify  | 0.027928   | 0.027928   | 0.027928   |   0.0 |  0.01
+Other   |            | 0.0159     |            |       |  0.01
+
+Nlocal:    1360 ave 1360 max 1360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7836 ave 7836 max 7836 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    249560 ave 249560 max 249560 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  1.00504e+06 ave 1.00504e+06 max 1.00504e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1005040
+Ave neighs/atom = 739
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:03:31
diff --git a/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.4 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.4
new file mode 100644
index 0000000000..7a0b7a269b
--- /dev/null
+++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.4
@@ -0,0 +1,142 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AA_prime_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (43.38 42.5773 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000224352 secs
+  read_data CPU = 0.00160909 secs
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group 		layer1 molecule 1
+680 atoms in group layer1
+group 		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff B N B N  # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn BNCH.ILP    B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair tersoff
+compute   	1 all pair coul/shield ecoul
+compute   	2 all pair ilp/graphene/hbn
+variable  	Tersoff  equal c_0     # Tersoff energy
+variable  	Ecoul    equal c_1     # Coulomb energy
+variable  	EILP     equal c_2     # total interlayer energy
+variable  	Evdw     equal c_2[1]  # attractive energy
+variable 	Erep     equal c_2[2]  # repulsive  energy
+
+############# Output ###############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+run 		1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  4 neighbor lists, perpetual/occasional/extra = 4 0 0
+  (1) pair tersoff, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (3) pair coul/shield, perpetual, skip from (4)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) neighbor class addition, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 18.99 | 18.99 | 18.99 Mbytes
+Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp 
+       0   -10193.138   -10245.837    52.699361   -77.557069    -10208.73   -36.776483    40.780586   -77.557069  -0.33075117          300 
+     100   -10192.814   -10215.193     22.37957   -80.997619   -10177.878   -36.967736    44.029884   -80.997619  -0.34809915    127.39947 
+     200   -10192.922   -10221.807    28.884855   -86.370319   -10184.251   -37.168986    49.201334   -86.370319  -0.38644764    164.43191 
+     300   -10192.878   -10219.029    26.151464   -83.063924   -10182.349    -36.30412    46.759804   -83.063924  -0.37660157    148.87162 
+     400   -10192.892   -10218.834    25.942229   -78.394242   -10181.398   -37.110968    41.283274   -78.394242  -0.32494569    147.68051 
+     500   -10192.909   -10221.331    28.422213   -81.768531    -10184.03   -36.946226    44.822304   -81.768531  -0.35489965    161.79824 
+     600   -10192.886   -10219.371     26.48495   -86.278335   -10182.669    -36.29515    49.983185   -86.278335  -0.40636253    150.77004 
+     700   -10192.902    -10220.95    28.048108    -82.28873   -10183.208    -37.39374     44.89499    -82.28873  -0.34777958    159.66859 
+     800    -10192.88    -10218.51    25.630186   -78.011019   -10181.427   -36.754209    41.256811   -78.011019  -0.32904942    145.90415 
+     900   -10192.894    -10220.56    27.665437   -82.474379   -10183.801   -36.381157    46.093222   -82.474379  -0.37703328    157.49017 
+    1000   -10192.897    -10219.01     26.11313   -87.125683   -10181.252   -37.361898    49.763785   -87.125683  -0.39607952    148.65339 
+Loop time of 68.3631 on 4 procs for 1000 steps with 1360 atoms
+
+Performance: 1.264 ns/day, 18.990 hours/ns, 14.628 timesteps/s
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 64.58      | 66.38      | 67.402     |  13.2 | 97.10
+Bond    | 0.0001719  | 0.00021869 | 0.00024033 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.93767    | 1.9601     | 3.76       |  77.0 |  2.87
+Output  | 0.00033593 | 0.00061601 | 0.0014501  |   0.0 |  0.00
+Modify  | 0.0085733  | 0.0089303  | 0.0093236  |   0.4 |  0.01
+Other   |            | 0.01285    |            |       |  0.02
+
+Nlocal:    340 ave 340 max 340 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    4536 ave 4536 max 4536 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    62390 ave 62390 max 62390 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  251260 ave 251260 max 251260 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1005040
+Ave neighs/atom = 739
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:01:08
diff --git a/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.1 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.1
new file mode 100644
index 0000000000..f9f1dedff6
--- /dev/null
+++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.1
@@ -0,0 +1,153 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       gr_hBN_Cstack_2L_noH.data
+  orthogonal box = (0 0 0) to (44.583 42.9 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1440 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000282049 secs
+  read_data CPU = 0.00159025 secs
+mass            1 10.8110   # boron    mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | membrane
+mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
+# Separate atom groups
+group 		hBN molecule 1
+720 atoms in group hBN
+group 		gr  molecule 2
+720 atoms in group gr
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo     NULL NULL C    # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * tersoff            BNC.tersoff B    N    NULL # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP    B    N    C    # long range
+pair_coeff  1 1 coul/shield 0.70
+pair_coeff  1 2 coul/shield 0.69498201415576216335
+pair_coeff  2 2 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair rebo
+compute   	1 all pair tersoff
+compute   	2 all pair ilp/graphene/hbn
+compute   	3 all pair coul/shield
+variable  	REBO     equal  c_0
+variable  	Tersoff  equal  c_1
+variable  	EILP     equal  c_2     # total interlayer energy
+variable  	Evdw     equal  c_2[1]  # attractive energy
+variable 	Erep     equal  c_2[2]  # repulsive  energy
+variable  	Ecoul    equal  c_3
+
+############# Output ##############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
+
+###### Run molecular dynamics ######
+run 		1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair rebo, perpetual, skip from (3)
+      attributes: full, newton on, ghost
+      pair build: skip/ghost
+      stencil: none
+      bin: none
+  (2) pair tersoff, perpetual, skip from (5)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (4) pair coul/shield, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton/skip
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, copy from (3)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) neighbor class addition, perpetual, half/full from (5)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 22.52 | 22.52 | 22.52 Mbytes
+Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp 
+       0   -10707.284   -10763.085    55.801605   -75.247726   -5401.7348   -5322.2781   -39.072409    36.175318   -75.247726            0          300 
+     100   -10707.074   -10737.127     30.05353   -73.217322   -5389.9568   -5309.2004   -37.970102     35.24722   -73.217322            0    161.57347 
+     200   -10707.016   -10734.932     27.91576   -71.603097   -5389.1294   -5307.7455   -38.056875    33.546222   -71.603097            0    150.08042 
+     300   -10707.013   -10734.987    27.973705   -75.082134   -5388.9196   -5308.1165   -37.950947    37.131186   -75.082134            0    150.39194 
+     400   -10707.012   -10735.498    28.486171   -76.339871   -5389.1657    -5308.153   -38.179442    38.160429   -76.339871            0    153.14706 
+     500   -10707.007   -10734.681    27.674101   -73.312354   -5388.7261   -5307.7384   -38.216944     35.09541   -73.312354            0    148.78121 
+     600   -10707.018   -10735.833    28.815132   -71.927763   -5389.0798    -5308.596   -38.157333     33.77043   -71.927763            0    154.91561 
+     700    -10707.02   -10735.656    28.635377   -74.679371   -5389.2971   -5308.1866   -38.172002    36.507368   -74.679371            0    153.94921 
+     800   -10707.004   -10734.352    27.347425   -76.371288   -5388.5923   -5307.7206   -38.038736    38.332552   -76.371288            0    147.02494 
+     900   -10707.014   -10735.832    28.817405   -73.699332   -5388.9674   -5308.7964   -38.068078    35.631254   -73.699332            0    154.92783 
+    1000   -10706.995   -10733.562     26.56615   -71.439868   -5388.0186   -5307.4414   -38.101452    33.338415   -71.439868            0    142.82466 
+Loop time of 152.66 on 1 procs for 1000 steps with 1440 atoms
+
+Performance: 0.566 ns/day, 42.406 hours/ns, 6.550 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 152.52     | 152.52     | 152.52     |   0.0 | 99.91
+Bond    | 0.00023174 | 0.00023174 | 0.00023174 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.087147   | 0.087147   | 0.087147   |   0.0 |  0.06
+Output  | 0.0004189  | 0.0004189  | 0.0004189  |   0.0 |  0.00
+Modify  | 0.029972   | 0.029972   | 0.029972   |   0.0 |  0.02
+Other   |            | 0.02057    |            |       |  0.01
+
+Nlocal:    1440 ave 1440 max 1440 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    8180 ave 8180 max 8180 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    140400 ave 140400 max 140400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  280800 ave 280800 max 280800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 280800
+Ave neighs/atom = 195
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:02:32
diff --git a/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.4 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.4
new file mode 100644
index 0000000000..a7b97a81b7
--- /dev/null
+++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.4
@@ -0,0 +1,153 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       gr_hBN_Cstack_2L_noH.data
+  orthogonal box = (0 0 0) to (44.583 42.9 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1440 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.00012207 secs
+  read_data CPU = 0.00357461 secs
+mass            1 10.8110   # boron    mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | membrane
+mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
+# Separate atom groups
+group 		hBN molecule 1
+720 atoms in group hBN
+group 		gr  molecule 2
+720 atoms in group gr
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo     NULL NULL C    # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * tersoff            BNC.tersoff B    N    NULL # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP    B    N    C    # long range
+pair_coeff  1 1 coul/shield 0.70
+pair_coeff  1 2 coul/shield 0.69498201415576216335
+pair_coeff  2 2 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair rebo
+compute   	1 all pair tersoff
+compute   	2 all pair ilp/graphene/hbn
+compute   	3 all pair coul/shield
+variable  	REBO     equal  c_0
+variable  	Tersoff  equal  c_1
+variable  	EILP     equal  c_2     # total interlayer energy
+variable  	Evdw     equal  c_2[1]  # attractive energy
+variable 	Erep     equal  c_2[2]  # repulsive  energy
+variable  	Ecoul    equal  c_3
+
+############# Output ##############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
+
+###### Run molecular dynamics ######
+run 		1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair rebo, perpetual, skip from (3)
+      attributes: full, newton on, ghost
+      pair build: skip/ghost
+      stencil: none
+      bin: none
+  (2) pair tersoff, perpetual, skip from (5)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (4) pair coul/shield, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton/skip
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, copy from (3)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) neighbor class addition, perpetual, half/full from (5)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 12.45 | 12.45 | 12.45 Mbytes
+Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp 
+       0   -10707.284   -10763.085    55.801605   -75.247726   -5401.7348   -5322.2781   -39.072409    36.175318   -75.247726            0          300 
+     100   -10707.074   -10737.127     30.05353   -73.217322   -5389.9568   -5309.2004   -37.970102     35.24722   -73.217322            0    161.57347 
+     200   -10707.016   -10734.932     27.91576   -71.603097   -5389.1294   -5307.7455   -38.056875    33.546222   -71.603097            0    150.08042 
+     300   -10707.013   -10734.987    27.973705   -75.082134   -5388.9196   -5308.1165   -37.950947    37.131186   -75.082134            0    150.39194 
+     400   -10707.012   -10735.498    28.486171   -76.339871   -5389.1657    -5308.153   -38.179442    38.160429   -76.339871            0    153.14706 
+     500   -10707.007   -10734.681    27.674101   -73.312354   -5388.7261   -5307.7384   -38.216944     35.09541   -73.312354            0    148.78121 
+     600   -10707.018   -10735.833    28.815132   -71.927763   -5389.0798    -5308.596   -38.157333     33.77043   -71.927763            0    154.91561 
+     700    -10707.02   -10735.656    28.635377   -74.679371   -5389.2971   -5308.1866   -38.172002    36.507368   -74.679371            0    153.94921 
+     800   -10707.004   -10734.352    27.347425   -76.371288   -5388.5923   -5307.7206   -38.038736    38.332552   -76.371288            0    147.02494 
+     900   -10707.014   -10735.832    28.817405   -73.699332   -5388.9674   -5308.7964   -38.068078    35.631254   -73.699332            0    154.92783 
+    1000   -10706.995   -10733.562     26.56615   -71.439868   -5388.0186   -5307.4414   -38.101452    33.338415   -71.439868            0    142.82466 
+Loop time of 54.095 on 4 procs for 1000 steps with 1440 atoms
+
+Performance: 1.597 ns/day, 15.026 hours/ns, 18.486 timesteps/s
+84.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 42.138     | 45.531     | 49.106     |  42.0 | 84.17
+Bond    | 0.0003159  | 0.00037384 | 0.000489   |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 4.71       | 8.2803     | 11.682     |  98.3 | 15.31
+Output  | 0.0021999  | 0.0055975  | 0.013382   |   6.0 |  0.01
+Modify  | 0.0092845  | 0.010981   | 0.012538   |   1.3 |  0.02
+Other   |            | 0.2673     |            |       |  0.49
+
+Nlocal:    360 ave 380 max 340 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    4716 ave 4736 max 4696 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    35100 ave 37050 max 33150 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+FullNghs:  70200 ave 74100 max 66300 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 280800
+Ave neighs/atom = 195
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:54
diff --git a/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.1 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.1
new file mode 100644
index 0000000000..1845c2e54d
--- /dev/null
+++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.1
@@ -0,0 +1,154 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use 2 atom types so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AB_stack_2L_noH_equi_300K.data
+  orthogonal box = (0 0 0) to (43.38 42.5773 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  reading velocities ...
+  1360 velocities
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000251532 secs
+  read_data CPU = 0.00451231 secs
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group membrane  type 1 2
+680 atoms in group membrane
+group adsorbate type 3 4
+680 atoms in group adsorbate
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff   NULL NULL B N  # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn BNCH-old.ILP  B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  0.001
+#velocity  adsorbate create 300.0 12345
+fix       subf membrane setforce 0.0 0.0 0.0
+fix       thermostat all nve
+
+compute   0 all pair tersoff
+compute   1 all pair coul/shield ecoul
+compute   2 all pair ilp/graphene/hbn
+variable  Tersoff  equal c_0
+variable  Ecoul    equal c_1
+variable  ILP      equal c_2
+variable  Evdw     equal c_2[1]
+variable  Erep     equal c_2[2]
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
+thermo_modify   lost warn #ignore
+
+#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
+#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
+
+###### Run molecular dynamics ######
+run 1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair tersoff, perpetual, skip from (4)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (3) pair coul/shield, perpetual, skip from (5)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) neighbor class addition, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, half/full from (4)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 54.59 | 54.59 | 54.59 Mbytes
+Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp 
+       0   -5114.6628   -5127.8586    13.195828   -5091.4121   -36.083114  -0.36343598    38.918674   -75.001787    75.119474 
+     100   -5114.6621   -5127.6958    13.033777   -5091.2408    -36.09276  -0.36228286    38.769906   -74.862666    74.196973 
+     200   -5114.6631   -5127.5945     12.93145   -5091.1508   -36.086669  -0.35708801     38.20076   -74.287429    73.614462 
+     300   -5114.6694   -5128.3286     13.65924   -5091.8646   -36.110786  -0.35328159    37.758284    -73.86907    77.757528 
+     400   -5114.6614   -5127.6424    12.980975   -5091.2348   -36.049634  -0.35794328    38.247252   -74.296886    73.896389 
+     500     -5114.66   -5127.4098    12.749794   -5090.9285   -36.119571  -0.36174976    38.745548   -74.865119    72.580351 
+     600   -5114.6673   -5128.0913    13.424021   -5091.6339    -36.09384  -0.36356991    38.927401   -75.021241    76.418503 
+     700    -5114.661   -5127.7467    13.085707   -5091.2811   -36.106639  -0.35892399    38.332616   -74.439255    74.492596 
+     800   -5114.6623    -5128.013    13.350778   -5091.5694   -36.089718  -0.35392503    37.851602    -73.94132    76.001554 
+     900   -5114.6675   -5128.1497    13.482146   -5091.6704   -36.124679  -0.35462869    37.885183   -74.009861    76.749392 
+    1000   -5114.6683   -5128.3365    13.668146    -5091.937   -36.037596  -0.36184347    38.709718   -74.747314    77.808228 
+Loop time of 207.028 on 1 procs for 1000 steps with 1360 atoms
+
+Performance: 0.417 ns/day, 57.508 hours/ns, 4.830 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 206.9      | 206.9      | 206.9      |   0.0 | 99.94
+Bond    | 0.00019169 | 0.00019169 | 0.00019169 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.081397   | 0.081397   | 0.081397   |   0.0 |  0.04
+Output  | 0.00036597 | 0.00036597 | 0.00036597 |   0.0 |  0.00
+Modify  | 0.033408   | 0.033408   | 0.033408   |   0.0 |  0.02
+Other   |            | 0.01615    |            |       |  0.01
+
+Nlocal:    1360 ave 1360 max 1360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7840 ave 7840 max 7840 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    249628 ave 249628 max 249628 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  253390 ave 253390 max 253390 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 253390
+Ave neighs/atom = 186.316
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:03:27
diff --git a/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.4 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.4
new file mode 100644
index 0000000000..ec2a8443a4
--- /dev/null
+++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.4
@@ -0,0 +1,154 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use 2 atom types so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AB_stack_2L_noH_equi_300K.data
+  orthogonal box = (0 0 0) to (43.38 42.5773 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  reading velocities ...
+  1360 velocities
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000332117 secs
+  read_data CPU = 0.00270581 secs
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group membrane  type 1 2
+680 atoms in group membrane
+group adsorbate type 3 4
+680 atoms in group adsorbate
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff   NULL NULL B N  # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn BNCH-old.ILP  B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  0.001
+#velocity  adsorbate create 300.0 12345
+fix       subf membrane setforce 0.0 0.0 0.0
+fix       thermostat all nve
+
+compute   0 all pair tersoff
+compute   1 all pair coul/shield ecoul
+compute   2 all pair ilp/graphene/hbn
+variable  Tersoff  equal c_0
+variable  Ecoul    equal c_1
+variable  ILP      equal c_2
+variable  Evdw     equal c_2[1]
+variable  Erep     equal c_2[2]
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
+thermo_modify   lost warn #ignore
+
+#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
+#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
+
+###### Run molecular dynamics ######
+run 1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair tersoff, perpetual, skip from (4)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (3) pair coul/shield, perpetual, skip from (5)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) neighbor class addition, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, half/full from (4)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 28.9 | 28.9 | 28.9 Mbytes
+Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp 
+       0   -5114.6628   -5127.8586    13.195828   -5091.4121   -36.083114  -0.36343598    38.918674   -75.001787    75.119474 
+     100   -5114.6621   -5127.6958    13.033777   -5091.2408    -36.09276  -0.36228286    38.769906   -74.862666    74.196973 
+     200   -5114.6631   -5127.5945     12.93145   -5091.1508   -36.086669  -0.35708801     38.20076   -74.287429    73.614462 
+     300   -5114.6694   -5128.3286     13.65924   -5091.8646   -36.110786  -0.35328159    37.758284    -73.86907    77.757528 
+     400   -5114.6614   -5127.6424    12.980975   -5091.2348   -36.049634  -0.35794328    38.247252   -74.296886    73.896389 
+     500     -5114.66   -5127.4098    12.749794   -5090.9285   -36.119571  -0.36174976    38.745548   -74.865119    72.580351 
+     600   -5114.6673   -5128.0913    13.424021   -5091.6339    -36.09384  -0.36356991    38.927401   -75.021241    76.418503 
+     700    -5114.661   -5127.7467    13.085707   -5091.2811   -36.106639  -0.35892399    38.332616   -74.439255    74.492596 
+     800   -5114.6623    -5128.013    13.350778   -5091.5694   -36.089718  -0.35392503    37.851602    -73.94132    76.001554 
+     900   -5114.6675   -5128.1497    13.482146   -5091.6704   -36.124679  -0.35462869    37.885183   -74.009861    76.749392 
+    1000   -5114.6683   -5128.3365    13.668146    -5091.937   -36.037596  -0.36184347    38.709718   -74.747314    77.808228 
+Loop time of 65.9005 on 4 procs for 1000 steps with 1360 atoms
+
+Performance: 1.311 ns/day, 18.306 hours/ns, 15.174 timesteps/s
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 63.244     | 64.208     | 65.281     |  10.1 | 97.43
+Bond    | 0.00013971 | 0.00017679 | 0.00022101 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.58237    | 1.6612     | 2.6292     |  63.1 |  2.52
+Output  | 0.0003171  | 0.00062358 | 0.0015192  |   0.0 |  0.00
+Modify  | 0.010251   | 0.010509   | 0.01075    |   0.2 |  0.02
+Other   |            | 0.02025    |            |       |  0.03
+
+Nlocal:    340 ave 346 max 336 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Nghost:    4537.5 ave 4540 max 4534 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs:    62407 ave 62413 max 62402 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+FullNghs:  63347.5 ave 65585 max 61866 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 253926
+Ave neighs/atom = 186.71
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:01:06
diff --git a/examples/USER/misc/kolmogorov_crespi_full/Bi_gr_AB_stack_2L_noH.data b/examples/USER/misc/kolmogorov_crespi_full/Bi_gr_AB_stack_2L_noH.data
new file mode 100644
index 0000000000..756123a6f1
--- /dev/null
+++ b/examples/USER/misc/kolmogorov_crespi_full/Bi_gr_AB_stack_2L_noH.data
@@ -0,0 +1,1372 @@
+ Generate Bi-layer graphene
+
+   1360  atoms
+
+ 2 atom types
+
+    0.000000000000000  42.599999999999994 xlo xhi
+    0.000000000000000  41.811706494712695 ylo yhi
+    0.000000000000000 100.000000000000000 zlo zhi
+
+ Atoms
+
+          1         1         1   0.000000000000000   0.000000000000000   1.229756073373903   0.000000000000000
+          2         1         1   0.000000000000000   0.710000000000000   0.000000000000000   0.000000000000000
+          3         1         1   0.000000000000000   2.130000000000000   0.000000000000000   0.000000000000000
+          4         1         1   0.000000000000000   2.840000000000000   1.229756073373903   0.000000000000000
+          5         1         1   0.000000000000000   4.260000000000000   1.229756073373903   0.000000000000000
+          6         1         1   0.000000000000000   4.970000000000000   0.000000000000000   0.000000000000000
+          7         1         1   0.000000000000000   6.390000000000000   0.000000000000000   0.000000000000000
+          8         1         1   0.000000000000000   7.100000000000000   1.229756073373903   0.000000000000000
+          9         1         1   0.000000000000000   8.520000000000000   1.229756073373903   0.000000000000000
+         10         1         1   0.000000000000000   9.230000000000000   0.000000000000000   0.000000000000000
+         11         1         1   0.000000000000000  10.649999999999999   0.000000000000000   0.000000000000000
+         12         1         1   0.000000000000000  11.359999999999999   1.229756073373903   0.000000000000000
+         13         1         1   0.000000000000000  12.779999999999999   1.229756073373903   0.000000000000000
+         14         1         1   0.000000000000000  13.489999999999998   0.000000000000000   0.000000000000000
+         15         1         1   0.000000000000000  14.910000000000000   0.000000000000000   0.000000000000000
+         16         1         1   0.000000000000000  15.619999999999999   1.229756073373903   0.000000000000000
+         17         1         1   0.000000000000000  17.039999999999999   1.229756073373903   0.000000000000000
+         18         1         1   0.000000000000000  17.750000000000000   0.000000000000000   0.000000000000000
+         19         1         1   0.000000000000000  19.169999999999998   0.000000000000000   0.000000000000000
+         20         1         1   0.000000000000000  19.879999999999999   1.229756073373903   0.000000000000000
+         21         1         1   0.000000000000000  21.299999999999997   1.229756073373903   0.000000000000000
+         22         1         1   0.000000000000000  22.009999999999998   0.000000000000000   0.000000000000000
+         23         1         1   0.000000000000000  23.429999999999996   0.000000000000000   0.000000000000000
+         24         1         1   0.000000000000000  24.139999999999997   1.229756073373903   0.000000000000000
+         25         1         1   0.000000000000000  25.559999999999999   1.229756073373903   0.000000000000000
+         26         1         1   0.000000000000000  26.270000000000000   0.000000000000000   0.000000000000000
+         27         1         1   0.000000000000000  27.689999999999998   0.000000000000000   0.000000000000000
+         28         1         1   0.000000000000000  28.399999999999999   1.229756073373903   0.000000000000000
+         29         1         1   0.000000000000000  29.820000000000000   1.229756073373903   0.000000000000000
+         30         1         1   0.000000000000000  30.530000000000001   0.000000000000000   0.000000000000000
+         31         1         1   0.000000000000000  31.949999999999999   0.000000000000000   0.000000000000000
+         32         1         1   0.000000000000000  32.659999999999997   1.229756073373903   0.000000000000000
+         33         1         1   0.000000000000000  34.079999999999998   1.229756073373903   0.000000000000000
+         34         1         1   0.000000000000000  34.789999999999999   0.000000000000000   0.000000000000000
+         35         1         1   0.000000000000000  36.210000000000001   0.000000000000000   0.000000000000000
+         36         1         1   0.000000000000000  36.920000000000002   1.229756073373903   0.000000000000000
+         37         1         1   0.000000000000000  38.339999999999996   1.229756073373903   0.000000000000000
+         38         1         1   0.000000000000000  39.049999999999997   0.000000000000000   0.000000000000000
+         39         1         1   0.000000000000000  40.469999999999999   0.000000000000000   0.000000000000000
+         40         1         1   0.000000000000000  41.179999999999993   1.229756073373903   0.000000000000000
+         41         1         1   0.000000000000000   0.000000000000000   3.689268220121709   0.000000000000000
+         42         1         1   0.000000000000000   0.710000000000000   2.459512146747806   0.000000000000000
+         43         1         1   0.000000000000000   2.130000000000000   2.459512146747806   0.000000000000000
+         44         1         1   0.000000000000000   2.840000000000000   3.689268220121709   0.000000000000000
+         45         1         1   0.000000000000000   4.260000000000000   3.689268220121709   0.000000000000000
+         46         1         1   0.000000000000000   4.970000000000000   2.459512146747806   0.000000000000000
+         47         1         1   0.000000000000000   6.390000000000000   2.459512146747806   0.000000000000000
+         48         1         1   0.000000000000000   7.100000000000000   3.689268220121709   0.000000000000000
+         49         1         1   0.000000000000000   8.520000000000000   3.689268220121709   0.000000000000000
+         50         1         1   0.000000000000000   9.230000000000000   2.459512146747806   0.000000000000000
+         51         1         1   0.000000000000000  10.649999999999999   2.459512146747806   0.000000000000000
+         52         1         1   0.000000000000000  11.359999999999999   3.689268220121709   0.000000000000000
+         53         1         1   0.000000000000000  12.779999999999999   3.689268220121709   0.000000000000000
+         54         1         1   0.000000000000000  13.489999999999998   2.459512146747806   0.000000000000000
+         55         1         1   0.000000000000000  14.910000000000000   2.459512146747806   0.000000000000000
+         56         1         1   0.000000000000000  15.619999999999999   3.689268220121709   0.000000000000000
+         57         1         1   0.000000000000000  17.039999999999999   3.689268220121709   0.000000000000000
+         58         1         1   0.000000000000000  17.750000000000000   2.459512146747806   0.000000000000000
+         59         1         1   0.000000000000000  19.169999999999998   2.459512146747806   0.000000000000000
+         60         1         1   0.000000000000000  19.879999999999999   3.689268220121709   0.000000000000000
+         61         1         1   0.000000000000000  21.299999999999997   3.689268220121709   0.000000000000000
+         62         1         1   0.000000000000000  22.009999999999998   2.459512146747806   0.000000000000000
+         63         1         1   0.000000000000000  23.429999999999996   2.459512146747806   0.000000000000000
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+       1196         2         2   0.000000000000000  38.340000000000003  30.743901834347572  3.3000000000000000
+       1197         2         2   0.000000000000000  39.759999999999998  30.743901834347572  3.3000000000000000
+       1198         2         2   0.000000000000000  40.469999999999999  29.514145760973669  3.3000000000000000
+       1199         2         2   0.000000000000000  41.890000000000001  29.514145760973669  3.3000000000000000
+       1200         2         2   0.000000000000000  42.599999999999994  30.743901834347572  3.3000000000000000
+       1201         2         2   0.000000000000000   1.420000000000000  33.203413981095380  3.3000000000000000
+       1202         2         2   0.000000000000000   2.130000000000000  31.973657907721474  3.3000000000000000
+       1203         2         2   0.000000000000000   3.550000000000000  31.973657907721474  3.3000000000000000
+       1204         2         2   0.000000000000000   4.260000000000000  33.203413981095380  3.3000000000000000
+       1205         2         2   0.000000000000000   5.680000000000000  33.203413981095380  3.3000000000000000
+       1206         2         2   0.000000000000000   6.390000000000000  31.973657907721474  3.3000000000000000
+       1207         2         2   0.000000000000000   7.810000000000000  31.973657907721474  3.3000000000000000
+       1208         2         2   0.000000000000000   8.520000000000000  33.203413981095380  3.3000000000000000
+       1209         2         2   0.000000000000000   9.940000000000000  33.203413981095380  3.3000000000000000
+       1210         2         2   0.000000000000000  10.650000000000000  31.973657907721474  3.3000000000000000
+       1211         2         2   0.000000000000000  12.069999999999999  31.973657907721474  3.3000000000000000
+       1212         2         2   0.000000000000000  12.779999999999999  33.203413981095380  3.3000000000000000
+       1213         2         2   0.000000000000000  14.199999999999999  33.203413981095380  3.3000000000000000
+       1214         2         2   0.000000000000000  14.909999999999998  31.973657907721474  3.3000000000000000
+       1215         2         2   0.000000000000000  16.329999999999998  31.973657907721474  3.3000000000000000
+       1216         2         2   0.000000000000000  17.039999999999999  33.203413981095380  3.3000000000000000
+       1217         2         2   0.000000000000000  18.460000000000001  33.203413981095380  3.3000000000000000
+       1218         2         2   0.000000000000000  19.170000000000002  31.973657907721474  3.3000000000000000
+       1219         2         2   0.000000000000000  20.589999999999996  31.973657907721474  3.3000000000000000
+       1220         2         2   0.000000000000000  21.299999999999997  33.203413981095380  3.3000000000000000
+       1221         2         2   0.000000000000000  22.719999999999999  33.203413981095380  3.3000000000000000
+       1222         2         2   0.000000000000000  23.430000000000000  31.973657907721474  3.3000000000000000
+       1223         2         2   0.000000000000000  24.849999999999994  31.973657907721474  3.3000000000000000
+       1224         2         2   0.000000000000000  25.559999999999995  33.203413981095380  3.3000000000000000
+       1225         2         2   0.000000000000000  26.979999999999997  33.203413981095380  3.3000000000000000
+       1226         2         2   0.000000000000000  27.689999999999998  31.973657907721474  3.3000000000000000
+       1227         2         2   0.000000000000000  29.109999999999999  31.973657907721474  3.3000000000000000
+       1228         2         2   0.000000000000000  29.820000000000000  33.203413981095380  3.3000000000000000
+       1229         2         2   0.000000000000000  31.240000000000002  33.203413981095380  3.3000000000000000
+       1230         2         2   0.000000000000000  31.950000000000003  31.973657907721474  3.3000000000000000
+       1231         2         2   0.000000000000000  33.369999999999997  31.973657907721474  3.3000000000000000
+       1232         2         2   0.000000000000000  34.079999999999998  33.203413981095380  3.3000000000000000
+       1233         2         2   0.000000000000000  35.500000000000000  33.203413981095380  3.3000000000000000
+       1234         2         2   0.000000000000000  36.210000000000001  31.973657907721474  3.3000000000000000
+       1235         2         2   0.000000000000000  37.630000000000003  31.973657907721474  3.3000000000000000
+       1236         2         2   0.000000000000000  38.340000000000003  33.203413981095380  3.3000000000000000
+       1237         2         2   0.000000000000000  39.759999999999998  33.203413981095380  3.3000000000000000
+       1238         2         2   0.000000000000000  40.469999999999999  31.973657907721474  3.3000000000000000
+       1239         2         2   0.000000000000000  41.890000000000001  31.973657907721474  3.3000000000000000
+       1240         2         2   0.000000000000000  42.599999999999994  33.203413981095380  3.3000000000000000
+       1241         2         2   0.000000000000000   1.420000000000000  35.662926127843185  3.3000000000000000
+       1242         2         2   0.000000000000000   2.130000000000000  34.433170054469279  3.3000000000000000
+       1243         2         2   0.000000000000000   3.550000000000000  34.433170054469279  3.3000000000000000
+       1244         2         2   0.000000000000000   4.260000000000000  35.662926127843185  3.3000000000000000
+       1245         2         2   0.000000000000000   5.680000000000000  35.662926127843185  3.3000000000000000
+       1246         2         2   0.000000000000000   6.390000000000000  34.433170054469279  3.3000000000000000
+       1247         2         2   0.000000000000000   7.810000000000000  34.433170054469279  3.3000000000000000
+       1248         2         2   0.000000000000000   8.520000000000000  35.662926127843185  3.3000000000000000
+       1249         2         2   0.000000000000000   9.940000000000000  35.662926127843185  3.3000000000000000
+       1250         2         2   0.000000000000000  10.650000000000000  34.433170054469279  3.3000000000000000
+       1251         2         2   0.000000000000000  12.069999999999999  34.433170054469279  3.3000000000000000
+       1252         2         2   0.000000000000000  12.779999999999999  35.662926127843185  3.3000000000000000
+       1253         2         2   0.000000000000000  14.199999999999999  35.662926127843185  3.3000000000000000
+       1254         2         2   0.000000000000000  14.909999999999998  34.433170054469279  3.3000000000000000
+       1255         2         2   0.000000000000000  16.329999999999998  34.433170054469279  3.3000000000000000
+       1256         2         2   0.000000000000000  17.039999999999999  35.662926127843185  3.3000000000000000
+       1257         2         2   0.000000000000000  18.460000000000001  35.662926127843185  3.3000000000000000
+       1258         2         2   0.000000000000000  19.170000000000002  34.433170054469279  3.3000000000000000
+       1259         2         2   0.000000000000000  20.589999999999996  34.433170054469279  3.3000000000000000
+       1260         2         2   0.000000000000000  21.299999999999997  35.662926127843185  3.3000000000000000
+       1261         2         2   0.000000000000000  22.719999999999999  35.662926127843185  3.3000000000000000
+       1262         2         2   0.000000000000000  23.430000000000000  34.433170054469279  3.3000000000000000
+       1263         2         2   0.000000000000000  24.849999999999994  34.433170054469279  3.3000000000000000
+       1264         2         2   0.000000000000000  25.559999999999995  35.662926127843185  3.3000000000000000
+       1265         2         2   0.000000000000000  26.979999999999997  35.662926127843185  3.3000000000000000
+       1266         2         2   0.000000000000000  27.689999999999998  34.433170054469279  3.3000000000000000
+       1267         2         2   0.000000000000000  29.109999999999999  34.433170054469279  3.3000000000000000
+       1268         2         2   0.000000000000000  29.820000000000000  35.662926127843185  3.3000000000000000
+       1269         2         2   0.000000000000000  31.240000000000002  35.662926127843185  3.3000000000000000
+       1270         2         2   0.000000000000000  31.950000000000003  34.433170054469279  3.3000000000000000
+       1271         2         2   0.000000000000000  33.369999999999997  34.433170054469279  3.3000000000000000
+       1272         2         2   0.000000000000000  34.079999999999998  35.662926127843185  3.3000000000000000
+       1273         2         2   0.000000000000000  35.500000000000000  35.662926127843185  3.3000000000000000
+       1274         2         2   0.000000000000000  36.210000000000001  34.433170054469279  3.3000000000000000
+       1275         2         2   0.000000000000000  37.630000000000003  34.433170054469279  3.3000000000000000
+       1276         2         2   0.000000000000000  38.340000000000003  35.662926127843185  3.3000000000000000
+       1277         2         2   0.000000000000000  39.759999999999998  35.662926127843185  3.3000000000000000
+       1278         2         2   0.000000000000000  40.469999999999999  34.433170054469279  3.3000000000000000
+       1279         2         2   0.000000000000000  41.890000000000001  34.433170054469279  3.3000000000000000
+       1280         2         2   0.000000000000000  42.599999999999994  35.662926127843185  3.3000000000000000
+       1281         2         2   0.000000000000000   1.420000000000000  38.122438274590991  3.3000000000000000
+       1282         2         2   0.000000000000000   2.130000000000000  36.892682201217085  3.3000000000000000
+       1283         2         2   0.000000000000000   3.550000000000000  36.892682201217085  3.3000000000000000
+       1284         2         2   0.000000000000000   4.260000000000000  38.122438274590991  3.3000000000000000
+       1285         2         2   0.000000000000000   5.680000000000000  38.122438274590991  3.3000000000000000
+       1286         2         2   0.000000000000000   6.390000000000000  36.892682201217085  3.3000000000000000
+       1287         2         2   0.000000000000000   7.810000000000000  36.892682201217085  3.3000000000000000
+       1288         2         2   0.000000000000000   8.520000000000000  38.122438274590991  3.3000000000000000
+       1289         2         2   0.000000000000000   9.940000000000000  38.122438274590991  3.3000000000000000
+       1290         2         2   0.000000000000000  10.650000000000000  36.892682201217085  3.3000000000000000
+       1291         2         2   0.000000000000000  12.069999999999999  36.892682201217085  3.3000000000000000
+       1292         2         2   0.000000000000000  12.779999999999999  38.122438274590991  3.3000000000000000
+       1293         2         2   0.000000000000000  14.199999999999999  38.122438274590991  3.3000000000000000
+       1294         2         2   0.000000000000000  14.909999999999998  36.892682201217085  3.3000000000000000
+       1295         2         2   0.000000000000000  16.329999999999998  36.892682201217085  3.3000000000000000
+       1296         2         2   0.000000000000000  17.039999999999999  38.122438274590991  3.3000000000000000
+       1297         2         2   0.000000000000000  18.460000000000001  38.122438274590991  3.3000000000000000
+       1298         2         2   0.000000000000000  19.170000000000002  36.892682201217085  3.3000000000000000
+       1299         2         2   0.000000000000000  20.589999999999996  36.892682201217085  3.3000000000000000
+       1300         2         2   0.000000000000000  21.299999999999997  38.122438274590991  3.3000000000000000
+       1301         2         2   0.000000000000000  22.719999999999999  38.122438274590991  3.3000000000000000
+       1302         2         2   0.000000000000000  23.430000000000000  36.892682201217085  3.3000000000000000
+       1303         2         2   0.000000000000000  24.849999999999994  36.892682201217085  3.3000000000000000
+       1304         2         2   0.000000000000000  25.559999999999995  38.122438274590991  3.3000000000000000
+       1305         2         2   0.000000000000000  26.979999999999997  38.122438274590991  3.3000000000000000
+       1306         2         2   0.000000000000000  27.689999999999998  36.892682201217085  3.3000000000000000
+       1307         2         2   0.000000000000000  29.109999999999999  36.892682201217085  3.3000000000000000
+       1308         2         2   0.000000000000000  29.820000000000000  38.122438274590991  3.3000000000000000
+       1309         2         2   0.000000000000000  31.240000000000002  38.122438274590991  3.3000000000000000
+       1310         2         2   0.000000000000000  31.950000000000003  36.892682201217085  3.3000000000000000
+       1311         2         2   0.000000000000000  33.369999999999997  36.892682201217085  3.3000000000000000
+       1312         2         2   0.000000000000000  34.079999999999998  38.122438274590991  3.3000000000000000
+       1313         2         2   0.000000000000000  35.500000000000000  38.122438274590991  3.3000000000000000
+       1314         2         2   0.000000000000000  36.210000000000001  36.892682201217085  3.3000000000000000
+       1315         2         2   0.000000000000000  37.630000000000003  36.892682201217085  3.3000000000000000
+       1316         2         2   0.000000000000000  38.340000000000003  38.122438274590991  3.3000000000000000
+       1317         2         2   0.000000000000000  39.759999999999998  38.122438274590991  3.3000000000000000
+       1318         2         2   0.000000000000000  40.469999999999999  36.892682201217085  3.3000000000000000
+       1319         2         2   0.000000000000000  41.890000000000001  36.892682201217085  3.3000000000000000
+       1320         2         2   0.000000000000000  42.599999999999994  38.122438274590991  3.3000000000000000
+       1321         2         2   0.000000000000000   1.420000000000000  40.581950421338796  3.3000000000000000
+       1322         2         2   0.000000000000000   2.130000000000000  39.352194347964890  3.3000000000000000
+       1323         2         2   0.000000000000000   3.550000000000000  39.352194347964890  3.3000000000000000
+       1324         2         2   0.000000000000000   4.260000000000000  40.581950421338796  3.3000000000000000
+       1325         2         2   0.000000000000000   5.680000000000000  40.581950421338796  3.3000000000000000
+       1326         2         2   0.000000000000000   6.390000000000000  39.352194347964890  3.3000000000000000
+       1327         2         2   0.000000000000000   7.810000000000000  39.352194347964890  3.3000000000000000
+       1328         2         2   0.000000000000000   8.520000000000000  40.581950421338796  3.3000000000000000
+       1329         2         2   0.000000000000000   9.940000000000000  40.581950421338796  3.3000000000000000
+       1330         2         2   0.000000000000000  10.650000000000000  39.352194347964890  3.3000000000000000
+       1331         2         2   0.000000000000000  12.069999999999999  39.352194347964890  3.3000000000000000
+       1332         2         2   0.000000000000000  12.779999999999999  40.581950421338796  3.3000000000000000
+       1333         2         2   0.000000000000000  14.199999999999999  40.581950421338796  3.3000000000000000
+       1334         2         2   0.000000000000000  14.909999999999998  39.352194347964890  3.3000000000000000
+       1335         2         2   0.000000000000000  16.329999999999998  39.352194347964890  3.3000000000000000
+       1336         2         2   0.000000000000000  17.039999999999999  40.581950421338796  3.3000000000000000
+       1337         2         2   0.000000000000000  18.460000000000001  40.581950421338796  3.3000000000000000
+       1338         2         2   0.000000000000000  19.170000000000002  39.352194347964890  3.3000000000000000
+       1339         2         2   0.000000000000000  20.589999999999996  39.352194347964890  3.3000000000000000
+       1340         2         2   0.000000000000000  21.299999999999997  40.581950421338796  3.3000000000000000
+       1341         2         2   0.000000000000000  22.719999999999999  40.581950421338796  3.3000000000000000
+       1342         2         2   0.000000000000000  23.430000000000000  39.352194347964890  3.3000000000000000
+       1343         2         2   0.000000000000000  24.849999999999994  39.352194347964890  3.3000000000000000
+       1344         2         2   0.000000000000000  25.559999999999995  40.581950421338796  3.3000000000000000
+       1345         2         2   0.000000000000000  26.979999999999997  40.581950421338796  3.3000000000000000
+       1346         2         2   0.000000000000000  27.689999999999998  39.352194347964890  3.3000000000000000
+       1347         2         2   0.000000000000000  29.109999999999999  39.352194347964890  3.3000000000000000
+       1348         2         2   0.000000000000000  29.820000000000000  40.581950421338796  3.3000000000000000
+       1349         2         2   0.000000000000000  31.240000000000002  40.581950421338796  3.3000000000000000
+       1350         2         2   0.000000000000000  31.950000000000003  39.352194347964890  3.3000000000000000
+       1351         2         2   0.000000000000000  33.369999999999997  39.352194347964890  3.3000000000000000
+       1352         2         2   0.000000000000000  34.079999999999998  40.581950421338796  3.3000000000000000
+       1353         2         2   0.000000000000000  35.500000000000000  40.581950421338796  3.3000000000000000
+       1354         2         2   0.000000000000000  36.210000000000001  39.352194347964890  3.3000000000000000
+       1355         2         2   0.000000000000000  37.630000000000003  39.352194347964890  3.3000000000000000
+       1356         2         2   0.000000000000000  38.340000000000003  40.581950421338796  3.3000000000000000
+       1357         2         2   0.000000000000000  39.759999999999998  40.581950421338796  3.3000000000000000
+       1358         2         2   0.000000000000000  40.469999999999999  39.352194347964890  3.3000000000000000
+       1359         2         2   0.000000000000000  41.890000000000001  39.352194347964890  3.3000000000000000
+       1360         2         2   0.000000000000000  42.599999999999994  40.581950421338796  3.3000000000000000
diff --git a/examples/USER/misc/kolmogorov_crespi_full/CH.KC b/examples/USER/misc/kolmogorov_crespi_full/CH.KC
new file mode 120000
index 0000000000..74f7f340e5
--- /dev/null
+++ b/examples/USER/misc/kolmogorov_crespi_full/CH.KC
@@ -0,0 +1 @@
+../../../../potentials/CH.KC
\ No newline at end of file
diff --git a/examples/USER/misc/kolmogorov_crespi_full/CH_taper.KC b/examples/USER/misc/kolmogorov_crespi_full/CH_taper.KC
new file mode 120000
index 0000000000..2693646814
--- /dev/null
+++ b/examples/USER/misc/kolmogorov_crespi_full/CH_taper.KC
@@ -0,0 +1 @@
+../../../../potentials/CH_taper.KC
\ No newline at end of file
diff --git a/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene b/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene
index c3e59337de..259604d953 100644
--- a/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene
+++ b/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene
@@ -5,21 +5,22 @@ atom_style      full
 processors      * * 1     # domain decomposition over x and y
 
 # System and atom definition
-# we use 2 atom types so that inter- and intra-layer
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
 # interactions can be specified separately
-# read lammps data file
-read_data       Bi_gr_AB_stack_2L_noH_300K.data
+
+read_data       Bi_gr_AB_stack_2L_noH.data
 mass            1 12.0107   # carbon mass (g/mole) | membrane
 mass            2 12.0107   # carbon mass (g/mole) | adsorbate
 # Separate atom groups
-group membrane  type 1
-group adsorbate type 2
+group		layer1 molecule 1
+group		layer2 molecule 2
 
 ######################## Potential defition ########################
-pair_style  hybrid/overlay  rebo  kolmogorov/crespi/full 16.0
+pair_style  hybrid/overlay  rebo  kolmogorov/crespi/full 16.0 1
 ####################################################################
-pair_coeff  * * rebo                     CH.rebo      NULL C  # chemical
-pair_coeff  * * kolmogorov/crespi/full   CC.KC-full     C    C  # long range
+pair_coeff  * * rebo               	 CH.rebo      C  C  # chemical
+pair_coeff  * * kolmogorov/crespi/full   CH_taper.KC  C  C  # long range
 ####################################################################
 # Neighbor update settings
 neighbor        2.0 bin
@@ -27,34 +28,25 @@ neigh_modify    every 1
 neigh_modify    delay 0
 neigh_modify    check yes
 
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
 #### Simulation settings ####
-timestep  0.001
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
+timestep	0.001
+velocity	all create 300.0 12345
 
-compute   0 all pair rebo
-compute   1 all pair kolmogorov/crespi/full
-variable  REBO     equal c_0
-variable  KC       equal c_1
+compute   	0 all pair rebo
+compute  	1 all pair kolmogorov/crespi/full
+variable  	REBO  equal c_0     # REBO energy
+variable  	KC    equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
 
 ############################
 
 # Output
 thermo          100
-thermo_style    custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn #ignore
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
+thermo_style    custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
+thermo_modify   line one format float %.16f
+thermo_modify   flush yes norm no lost warn
 
 ###### Run molecular dynamics ######
-run 1000
+fix       	thermostat all nve
+run 	  	1000
diff --git a/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.1 b/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.1
new file mode 100644
index 0000000000..f400df565c
--- /dev/null
+++ b/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.1
@@ -0,0 +1,129 @@
+LAMMPS (5 Jun 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+
+read_data       Bi_gr_AB_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (42.6 41.8117 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000143357 secs
+  read_data CPU = 0.00128686 secs
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Separate atom groups
+group		layer1 molecule 1
+680 atoms in group layer1
+group		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  kolmogorov/crespi/full 16.0 1
+####################################################################
+pair_coeff  * * rebo               	 CH.rebo      C  C  # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * kolmogorov/crespi/full   CH_taper.KC  C  C  # long range
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep	0.001
+velocity	all create 300.0 12345
+
+compute   	0 all pair rebo
+compute  	1 all pair kolmogorov/crespi/full
+variable  	REBO  equal c_0     # REBO energy
+variable  	KC    equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
+thermo_modify   line one format float %.16f
+thermo_modify   flush yes norm no lost warn
+
+###### Run molecular dynamics ######
+fix       	thermostat all nve
+run 	  	1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair kolmogorov/crespi/full, perpetual, copy from (1)
+      attributes: full, newton on, ghost
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes
+Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp 
+       0 0.0000000000000000 -10037.7640583248121402 -10090.4634194413119985 52.6993611164999436 -10057.1894932863488066 -33.2739261549639664 35.9559834316876348 -69.2299095866357561 299.9999999999996589 
+     100 5.3877589240437374 -10037.5122858156355505 -10065.4637593850693520 27.9514735694345475 -10032.2132655062632693 -33.2504938788055995 25.2100699045900747 -58.4605637833913789 159.1184768311149185 
+     200 10.7755050340201706 -10037.4414086674350983 -10061.6271012692632212 24.1856926018286202 -10028.9093252939674130 -32.7177759752951403 18.5366534598604176 -51.2544294351563394 137.6811336385792970 
+     300 16.1665089030284435 -10037.4824653300311184 -10064.2845326005663082 26.8020672705344225 -10030.9195389405322203 -33.3649936600345924 26.3639208740001152 -59.7289145340284122 152.5752876469470891 
+     400 21.5454839280573651 -10037.5105626329259394 -10064.8769084956420556 27.3663458627154164 -10031.8478821022799821 -33.0290263933626349 36.6142885774199272 -69.6433149707719963 155.7875386888538571 
+     500 26.9370588400634006 -10037.5010433785082569 -10064.8363209936451312 27.3352776151367571 -10031.4417172103931080 -33.3946037832518243 26.2980262321670750 -59.6926300154142595 155.6106774503846850 
+     600 32.4204196080099791 -10037.4817772372425679 -10064.1925798287738871 26.7108025915316247 -10031.4376178099264507 -32.7549620188478201 18.5745873777024606 -51.3295493965519327 152.0557480714992380 
+     700 37.8001567909959704 -10037.4834430268438155 -10064.1291975032218033 26.6457544763788299 -10030.8722888097800023 -33.2569086934421492 25.2322818106646771 -58.4891905041015008 151.6854507067418467 
+     800 43.1622281169984490 -10037.5047888097760733 -10064.8671187128948077 27.3623299031188978 -10031.9815058608437539 -32.8856128520517217 36.5236695083771536 -69.4092823604148350 155.7646771616279011 
+     900 48.5261204120470211 -10037.5068323940176924 -10065.3998155271074211 27.8929831330889542 -10032.1734374829957233 -33.2263780441125931 27.7314849391008309 -60.9578629832065317 158.7855101588076820 
+    1000 53.8888844919856638 -10037.4811494880468672 -10064.0099109142265661 26.5287614261789670 -10031.3325267421259923 -32.6773841721003464 18.9005970229871600 -51.5779811950879434 151.0194480396057202 
+Loop time of 53.8889 on 1 procs for 1000 steps with 1360 atoms
+
+Performance: 1.603 ns/day, 14.969 hours/ns, 18.557 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 53.836     | 53.836     | 53.836     |   0.0 | 99.90
+Bond    | 0.00043479 | 0.00043479 | 0.00043479 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.032452   | 0.032452   | 0.032452   |   0.0 |  0.06
+Output  | 0.00058326 | 0.00058326 | 0.00058326 |   0.0 |  0.00
+Modify  | 0.0094135  | 0.0094135  | 0.0094135  |   0.0 |  0.02
+Other   |            | 0.009815   |            |       |  0.02
+
+Nlocal:    1360 ave 1360 max 1360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7964 ave 7964 max 7964 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  1.037e+06 ave 1.037e+06 max 1.037e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037000
+Ave neighs/atom = 762.5
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:54
diff --git a/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.4 b/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.4
new file mode 100644
index 0000000000..ebb2c8c3fa
--- /dev/null
+++ b/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.4
@@ -0,0 +1,129 @@
+LAMMPS (5 Jun 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+
+read_data       Bi_gr_AB_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (42.6 41.8117 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000245051 secs
+  read_data CPU = 0.00257704 secs
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Separate atom groups
+group		layer1 molecule 1
+680 atoms in group layer1
+group		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  kolmogorov/crespi/full 16.0 1
+####################################################################
+pair_coeff  * * rebo               	 CH.rebo      C  C  # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * kolmogorov/crespi/full   CH_taper.KC  C  C  # long range
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep	0.001
+velocity	all create 300.0 12345
+
+compute   	0 all pair rebo
+compute  	1 all pair kolmogorov/crespi/full
+variable  	REBO  equal c_0     # REBO energy
+variable  	KC    equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
+thermo_modify   line one format float %.16f
+thermo_modify   flush yes norm no lost warn
+
+###### Run molecular dynamics ######
+fix       	thermostat all nve
+run 	  	1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair kolmogorov/crespi/full, perpetual, copy from (1)
+      attributes: full, newton on, ghost
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.878 | 9.878 | 9.878 Mbytes
+Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp 
+       0 0.0000000000000000 -10037.7640583250176860 -10090.4634194415175443 52.6993611164999933 -10057.1894932866325689 -33.2739261548851388 35.9559834317043467 -69.2299095866038954 299.9999999999999432 
+     100 1.5180600649910048 -10037.5122858156355505 -10065.4637593850711710 27.9514735694348637 -10032.2132655062741833 -33.2504938787968172 25.2100699046001573 -58.4605637833912795 159.1184768311167090 
+     200 3.0089348420733586 -10037.4414086674296414 -10061.6271012692577642 24.1856926018279914 -10028.9093252939601371 -32.7177759752976272 18.5366534598677504 -51.2544294351567515 137.6811336385757158 
+     300 4.5315427089808509 -10037.4824653300020145 -10064.2845326005372044 26.8020672705348311 -10030.9195389405158494 -33.3649936600211205 26.3639208740115549 -59.7289145340278722 152.5752876469494197 
+     400 6.0353655620710924 -10037.5105626329095685 -10064.8769084956238657 27.3663458627148124 -10031.8478821022818011 -33.0290263933414394 36.6142885774347562 -69.6433149707726074 155.7875386888504181 
+     500 7.5396006110822782 -10037.5010433784900670 -10064.8363209936269413 27.3352776151361780 -10031.4417172103858320 -33.3946037832416351 26.2980262321774489 -59.6926300154146787 155.6106774503813881 
+     600 9.2617433650884777 -10037.4817772372534819 -10064.1925798287848011 26.7108025915320830 -10031.4376178099319077 -32.7549620188514226 18.5745873777100208 -51.3295493965524017 152.0557480715018528 
+     700 10.7484918619738892 -10037.4834430268347205 -10064.1291975032127084 26.6457544763787268 -10030.8722888097836403 -33.2569086934306739 25.2322818106757047 -58.4891905041008613 151.6854507067412499 
+     800 12.2509897360578179 -10037.5047888097869873 -10064.8671187129039026 27.3623299031166667 -10031.9815058608728577 -32.8856128520297801 36.5236695083899718 -69.4092823604150908 155.7646771616151966 
+     900 13.7584852169966325 -10037.5068323939758557 -10065.3998155270637653 27.8929831330881477 -10032.1734374829648004 -33.2263780440982259 27.7314849391120788 -60.9578629832060841 158.7855101588031062 
+    1000 15.2755981830414385 -10037.4811494880432292 -10064.0099109142211091 26.5287614261777058 -10031.3325267421205353 -32.6773841721017888 18.9005970229946634 -51.5779811950868776 151.0194480395985295 
+Loop time of 15.2757 on 4 procs for 1000 steps with 1360 atoms
+
+Performance: 5.656 ns/day, 4.243 hours/ns, 65.464 timesteps/s
+99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 13.985     | 14.446     | 14.823     |   7.9 | 94.57
+Bond    | 0.00040979 | 0.00042456 | 0.00046059 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.43692    | 0.81428    | 1.2749     |  33.2 |  5.33
+Output  | 0.00028016 | 0.00037143 | 0.00063561 |   0.0 |  0.00
+Modify  | 0.0045586  | 0.0046468  | 0.0047903  |   0.1 |  0.03
+Other   |            | 0.01041    |            |       |  0.07
+
+Nlocal:    340 ave 340 max 340 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    4628 ave 4628 max 4628 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  259250 ave 259250 max 259250 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037000
+Ave neighs/atom = 762.5
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:15
diff --git a/examples/USER/misc/momentum/in.momentum b/examples/USER/misc/momentum/in.momentum
new file mode 100644
index 0000000000..5adcbfeff6
--- /dev/null
+++ b/examples/USER/misc/momentum/in.momentum
@@ -0,0 +1,65 @@
+# Test compute momentum with by comparing it's output with compute reduce
+
+# Script will output the two computations of the total momentum as
+# thermo vars - they should be identical
+
+# 3D LJ Poiseuille flow simulation
+dimension	3
+boundary	p p p
+
+atom_style	atomic
+neighbor	0.3 bin
+neigh_modify	delay 5
+
+# create geometry
+lattice		hcp 0.5
+region		box block 0 20 0 10 0 10
+create_box	3 box
+create_atoms	1 box
+
+mass		1 1.0
+mass		2 1.0
+mass		3 1.0
+
+# LJ potentials
+pair_style	lj/cut 1.0
+pair_coeff	* * 1.0 1.0 1.0
+
+# define groups
+region	     1 block INF INF INF 1.0 INF INF
+group	     lower region 1
+region	     2 block INF INF 9.0 INF INF INF
+group	     upper region 2
+group	     boundary union lower upper
+group	     liquid subtract all boundary
+
+set	     group lower type 2
+set	     group upper type 3
+
+# temperature settings
+compute      mobile liquid temp
+velocity     liquid create 1.0 100 temp mobile
+fix          1 all nve
+fix          2 liquid temp/rescale 200 1.0 2.0 0.02 1.0
+fix_modify   2 temp mobile
+
+velocity     boundary set 0.0 0.0 0.0
+fix	     4 lower setforce 0.0 0.0 0.0
+fix	     5 upper setforce 0.0 0.0 0.0
+fix	     6 liquid addforce 0.1 0.0 0.0
+
+# Compute total momentum
+compute mom liquid momentum
+
+# Comparison (momentum variables + compute reduce)
+variable mx atom mass*vx
+variable my atom mass*vy
+variable mz atom mass*vz
+compute mom_red liquid reduce sum v_mx v_my v_mz
+
+# Run
+timestep	0.003
+thermo		1000
+thermo_style custom step c_mom_red[*] c_mom[*]
+
+run		100000
diff --git a/examples/kim/.gitignore b/examples/kim/.gitignore
new file mode 100644
index 0000000000..63421e4217
--- /dev/null
+++ b/examples/kim/.gitignore
@@ -0,0 +1 @@
+/kim.log
diff --git a/examples/kim/in.kim.lj.newton-on b/examples/kim/in.kim-ex.melt
similarity index 79%
rename from examples/kim/in.kim.lj.newton-on
rename to examples/kim/in.kim-ex.melt
index 3a95f1dbb0..5cc3dbc61b 100644
--- a/examples/kim/in.kim.lj.newton-on
+++ b/examples/kim/in.kim-ex.melt
@@ -14,20 +14,14 @@ variable	xx equal 20*$x
 variable	yy equal 20*$y
 variable	zz equal 20*$z
 
-units		metal
-atom_style	atomic
-newton          on
+kim_init	LennardJones_Ar real
 
 lattice		fcc 4.4300
 region		box block 0 ${xx} 0 ${yy} 0 ${zz}
 create_box	1 box
 create_atoms	1 box
 
-#pair_style	lj/cut 8.1500
-#pair_coeff	1 1 0.0104 3.4000
-
-pair_style      kim LennardJones_Ar
-pair_coeff      * * Ar
+kim_interactions Ar
 
 mass		1 39.95
 velocity	all create 200.0 232345 loop geom
diff --git a/examples/kim/in.kim-pm-query.melt b/examples/kim/in.kim-pm-query.melt
new file mode 100644
index 0000000000..fa04d90436
--- /dev/null
+++ b/examples/kim/in.kim-pm-query.melt
@@ -0,0 +1,46 @@
+# 3d Lennard-Jones melt
+#
+# This example requires that the KIM Portable Model (PM)
+# SW_StillingerWeber_1985_Si__MO_405512056662_005
+# is installed.  This can be done with the command
+#   kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
+# If this command does not work, you may need to setup your PATH to find the utility.
+# If you installed the kim-api using the LAMMPS CMake build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS build directory)
+#   source ./kim_build-prefix/bin/kim-api-activate
+# If you installed the kim-api using the LAMMPS Make build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS src directory)
+#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
+# (where you should relplace X.Y.Z with the appropriate kim-api version number).
+#
+# Or, see https://openkim.org/doc/obtaining-models for alternative options.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+kim_init	SW_StillingerWeber_1985_Si__MO_405512056662_005 real
+kim_query       a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
+
+lattice		fcc ${a0}
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+
+kim_interactions Si
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100
diff --git a/examples/kim/in.kim-pm.melt b/examples/kim/in.kim-pm.melt
new file mode 100644
index 0000000000..9959a66793
--- /dev/null
+++ b/examples/kim/in.kim-pm.melt
@@ -0,0 +1,45 @@
+# 3d Lennard-Jones melt
+#
+# This example requires that the KIM Portable Model (PM)
+# SW_StillingerWeber_1985_Si__MO_405512056662_005
+# is installed.  This can be done with the command
+#   kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
+# If this command does not work, you may need to setup your PATH to find the utility.
+# If you installed the kim-api using the LAMMPS CMake build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS build directory)
+#   source ./kim_build-prefix/bin/kim-api-activate
+# If you installed the kim-api using the LAMMPS Make build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS src directory)
+#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
+# (where you should relplace X.Y.Z with the appropriate kim-api version number).
+#
+# Or, see https://openkim.org/doc/obtaining-models for alternative options.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+kim_init	SW_StillingerWeber_1985_Si__MO_405512056662_005 real
+
+lattice		fcc 4.4300
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+
+kim_interactions Si
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100
diff --git a/examples/kim/in.kim-sm.melt b/examples/kim/in.kim-sm.melt
new file mode 100644
index 0000000000..0ee8e9a857
--- /dev/null
+++ b/examples/kim/in.kim-sm.melt
@@ -0,0 +1,45 @@
+# 3d Lennard-Jones melt
+#
+# This example requires that the KIM Simulator Model (PM)
+# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
+# is installed.  This can be done with the command
+#   kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
+# If this command does not work, you may need to setup your PATH to find the utility.
+# If you installed the kim-api using the LAMMPS CMake build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS build directory)
+#   source ./kim_build-prefix/bin/kim-api-activate
+# If you installed the kim-api using the LAMMPS Make build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS src directory)
+#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
+# (where you should relplace X.Y.Z with the appropriate kim-api version number).
+#
+# See https://openkim.org/doc/obtaining-models for alternative options.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+kim_init	Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
+
+lattice		fcc 4.4300
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+
+kim_interactions O
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100
diff --git a/examples/kim/in.kim.lj.lmp.newton-off b/examples/kim/in.kim.lj.lmp.newton-off
deleted file mode 100644
index 197755294a..0000000000
--- a/examples/kim/in.kim.lj.lmp.newton-off
+++ /dev/null
@@ -1,35 +0,0 @@
-# 3d Lennard-Jones melt
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
-
-units		metal
-atom_style	atomic
-newton          off
-
-lattice		fcc 4.4300
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
-
-pair_style	lj/cut 8.1500
-pair_coeff	1 1 0.0104 3.4000
-
-#pair_style      kim LennardJones_Ar
-#pair_coeff      * * Ar
-
-mass		1 39.95
-velocity	all create 200.0 232345 loop geom
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 all nve
-#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
-
-run 		100
diff --git a/examples/kim/in.kim.lj.newton-off b/examples/kim/in.kim.lj.newton-off
deleted file mode 100644
index 82cf5ba602..0000000000
--- a/examples/kim/in.kim.lj.newton-off
+++ /dev/null
@@ -1,41 +0,0 @@
-# 3d Lennard-Jones melt
-#
-# This example requires that the example models provided with
-# the kim-api package are installed.  see the ./lib/kim/README or
-# ./lib/kim/Install.py files for details on how to install these
-# example models.
-#
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
-
-units		metal
-atom_style	atomic
-newton          off
-
-lattice		fcc 4.4300
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
-
-#pair_style	lj/cut 8.1500
-#pair_coeff	1 1 0.0104 3.4000
-
-pair_style      kim LennardJones_Ar
-pair_coeff      * * Ar
-
-mass		1 39.95
-velocity	all create 200.0 232345 loop geom
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
-
-fix		1 all nve
-#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
-
-run 		100
diff --git a/examples/kim/in.kim.lj.lmp.newton-on b/examples/kim/in.lammps.melt
similarity index 91%
rename from examples/kim/in.kim.lj.lmp.newton-on
rename to examples/kim/in.lammps.melt
index f9f79e2bb2..5792f3a5db 100644
--- a/examples/kim/in.kim.lj.lmp.newton-on
+++ b/examples/kim/in.lammps.melt
@@ -8,9 +8,7 @@ variable	xx equal 20*$x
 variable	yy equal 20*$y
 variable	zz equal 20*$z
 
-units		metal
-atom_style	atomic
-newton          on
+units		real
 
 lattice		fcc 4.4300
 region		box block 0 ${xx} 0 ${yy} 0 ${zz}
diff --git a/examples/kim/in.query b/examples/kim/in.query
deleted file mode 100644
index 33272dc298..0000000000
--- a/examples/kim/in.query
+++ /dev/null
@@ -1,11 +0,0 @@
-
-# example for performing a query to the OpenKIM test database to retrieve
-# a parameter to be used in the input. here it requests the aluminium
-# lattice constant for a specific test used for a specific model and then
-# assigns it to the variable 'latconst'
-
-units metal
-info variables out log
-kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
-info variables out log
-lattice fcc ${latconst}
diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1
deleted file mode 100644
index 5925fd750d..0000000000
--- a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1
+++ /dev/null
@@ -1,55 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 1 by 1 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.004499 secs
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton off
-      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 20.37 | 20.37 | 20.37 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 2.92885 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 2.950 ns/day, 8.136 hours/ns, 34.143 timesteps/s
-99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.5638     | 2.5638     | 2.5638     |   0.0 | 87.54
-Neigh   | 0.31935    | 0.31935    | 0.31935    |   0.0 | 10.90
-Comm    | 0.006833   | 0.006833   | 0.006833   |   0.0 |  0.23
-Output  | 0.000107   | 0.000107   | 0.000107   |   0.0 |  0.00
-Modify  | 0.027806   | 0.027806   | 0.027806   |   0.0 |  0.95
-Other   |            | 0.01091    |            |       |  0.37
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19911 ave 19911 max 19911 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    2.3705e+06 ave 2.3705e+06 max 2.3705e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 2370499
-Ave neighs/atom = 74.0781
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:03
diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4
deleted file mode 100644
index c1ca108c7b..0000000000
--- a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4
+++ /dev/null
@@ -1,55 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 2 by 2 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.001039 secs
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton off
-      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 8.013 | 8.013 | 8.013 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 0.778581 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 11.097 ns/day, 2.163 hours/ns, 128.439 timesteps/s
-99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.65171    | 0.65891    | 0.67656    |   1.3 | 84.63
-Neigh   | 0.07924    | 0.079548   | 0.07997    |   0.1 | 10.22
-Comm    | 0.006755   | 0.0069015  | 0.007072   |   0.2 |  0.89
-Output  | 4.6e-05    | 9.725e-05  | 0.000203   |   0.0 |  0.01
-Modify  | 0.006841   | 0.006941   | 0.007015   |   0.1 |  0.89
-Other   |            | 0.02618    |            |       |  3.36
-
-Nlocal:    8000 ave 8018 max 7967 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Nghost:    9131 ave 9164 max 9113 min
-Histogram: 2 0 0 1 0 0 0 0 0 1
-Neighs:    630904 ave 632094 max 628209 min
-Histogram: 1 0 0 0 0 0 0 1 0 2
-
-Total # of neighbors = 2523614
-Ave neighs/atom = 78.8629
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1
deleted file mode 100644
index 53555743d7..0000000000
--- a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1
+++ /dev/null
@@ -1,55 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 1 by 1 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.003479 secs
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 2.17978 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 3.964 ns/day, 6.055 hours/ns, 45.876 timesteps/s
-99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.9892     | 1.9892     | 1.9892     |   0.0 | 91.26
-Neigh   | 0.14506    | 0.14506    | 0.14506    |   0.0 |  6.65
-Comm    | 0.011049   | 0.011049   | 0.011049   |   0.0 |  0.51
-Output  | 9.1e-05    | 9.1e-05    | 9.1e-05    |   0.0 |  0.00
-Modify  | 0.02347    | 0.02347    | 0.02347    |   0.0 |  1.08
-Other   |            | 0.01094    |            |       |  0.50
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19911 ave 19911 max 19911 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    2.12688e+06 ave 2.12688e+06 max 2.12688e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 2126875
-Ave neighs/atom = 66.4648
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:02
diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4
deleted file mode 100644
index f0fdf66193..0000000000
--- a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4
+++ /dev/null
@@ -1,55 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 2 by 2 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.000919 secs
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 7.632 | 7.632 | 7.632 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 0.63515 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 13.603 ns/day, 1.764 hours/ns, 157.443 timesteps/s
-99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.55365    | 0.5566     | 0.55868    |   0.2 | 87.63
-Neigh   | 0.041495   | 0.0418     | 0.04211    |   0.1 |  6.58
-Comm    | 0.019086   | 0.021075   | 0.023898   |   1.2 |  3.32
-Output  | 4.4e-05    | 5.025e-05  | 6e-05      |   0.0 |  0.01
-Modify  | 0.009315   | 0.0093595  | 0.009422   |   0.0 |  1.47
-Other   |            | 0.006263   |            |       |  0.99
-
-Nlocal:    8000 ave 8018 max 7967 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Nghost:    9131 ave 9164 max 9113 min
-Histogram: 2 0 0 1 0 0 0 0 0 1
-Neighs:    531719 ave 533273 max 529395 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-
-Total # of neighbors = 2126875
-Ave neighs/atom = 66.4648
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.1 b/examples/kim/log.06Feb2019.in.kim.lj.newton-off.1
deleted file mode 100644
index 0ab258fe0d..0000000000
--- a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.1
+++ /dev/null
@@ -1,59 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 1 by 1 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.003446 secs
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair kim, perpetual
-      attributes: full, newton off, cut 8.45
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 28.51 | 28.51 | 28.51 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 3.01669 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 2.864 ns/day, 8.380 hours/ns, 33.149 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.6562     | 2.6562     | 2.6562     |   0.0 | 88.05
-Neigh   | 0.31903    | 0.31903    | 0.31903    |   0.0 | 10.58
-Comm    | 0.00634    | 0.00634    | 0.00634    |   0.0 |  0.21
-Output  | 9.1e-05    | 9.1e-05    | 9.1e-05    |   0.0 |  0.00
-Modify  | 0.024723   | 0.024723   | 0.024723   |   0.0 |  0.82
-Other   |            | 0.01032    |            |       |  0.34
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19911 ave 19911 max 19911 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 4253750
-Ave neighs/atom = 132.93
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:03
diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.4 b/examples/kim/log.06Feb2019.in.kim.lj.newton-off.4
deleted file mode 100644
index c17ea6afb7..0000000000
--- a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.4
+++ /dev/null
@@ -1,65 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 2 by 2 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.000921 secs
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair kim, perpetual
-      attributes: full, newton off, cut 8.45
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 10.05 | 10.05 | 10.05 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 0.890192 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 9.706 ns/day, 2.473 hours/ns, 112.335 timesteps/s
-99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.77867    | 0.77906    | 0.7794     |   0.0 | 87.52
-Neigh   | 0.087831   | 0.088176   | 0.088805   |   0.1 |  9.91
-Comm    | 0.006358   | 0.0065898  | 0.006815   |   0.3 |  0.74
-Output  | 4.9e-05    | 5.975e-05  | 6.8e-05    |   0.0 |  0.01
-Modify  | 0.010265   | 0.010429   | 0.010678   |   0.2 |  1.17
-Other   |            | 0.005874   |            |       |  0.66
-
-Nlocal:    8000 ave 8018 max 7967 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Nghost:    9131 ave 9164 max 9113 min
-Histogram: 2 0 0 1 0 0 0 0 0 1
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-
-Total # of neighbors = 4253750
-Ave neighs/atom = 132.93
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.1 b/examples/kim/log.06Feb2019.in.kim.lj.newton-on.1
deleted file mode 100644
index 59d018e12a..0000000000
--- a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.1
+++ /dev/null
@@ -1,59 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 1 by 1 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.003089 secs
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair kim, perpetual
-      attributes: full, newton off, cut 8.45
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 3.05849 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 2.825 ns/day, 8.496 hours/ns, 32.696 timesteps/s
-99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.6786     | 2.6786     | 2.6786     |   0.0 | 87.58
-Neigh   | 0.33105    | 0.33105    | 0.33105    |   0.0 | 10.82
-Comm    | 0.012602   | 0.012602   | 0.012602   |   0.0 |  0.41
-Output  | 9.5e-05    | 9.5e-05    | 9.5e-05    |   0.0 |  0.00
-Modify  | 0.024858   | 0.024858   | 0.024858   |   0.0 |  0.81
-Other   |            | 0.01132    |            |       |  0.37
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    19911 ave 19911 max 19911 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 4253750
-Ave neighs/atom = 132.93
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:03
diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.4 b/examples/kim/log.06Feb2019.in.kim.lj.newton-on.4
deleted file mode 100644
index da8c9f0faa..0000000000
--- a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.4
+++ /dev/null
@@ -1,65 +0,0 @@
-LAMMPS (1 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
-  using 1 OpenMP thread(s) per MPI task
-Lattice spacing in x,y,z = 4.43 4.43 4.43
-Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
-  1 by 2 by 2 MPI processor grid
-Created 32000 atoms
-  Time spent = 0.000893 secs
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
-WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.45
-  ghost atom cutoff = 8.45
-  binsize = 4.225, bins = 21 21 21
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair kim, perpetual
-      attributes: full, newton off, cut 8.45
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Setting up Verlet run ...
-  Unit style    : metal
-  Current step  : 0
-  Time step     : 0.001
-Per MPI rank memory allocation (min/avg/max) = 9.789 | 9.789 | 9.789 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          200    6290.8194            0    7118.0584    129712.25 
-     100    95.179725     6718.814            0     7112.496    133346.59 
-Loop time of 0.903182 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 9.566 ns/day, 2.509 hours/ns, 110.720 timesteps/s
-99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.76173    | 0.76349    | 0.76597    |   0.2 | 84.53
-Neigh   | 0.088773   | 0.088938   | 0.089074   |   0.0 |  9.85
-Comm    | 0.032018   | 0.03452    | 0.03638    |   0.9 |  3.82
-Output  | 4e-05      | 4.425e-05  | 5.2e-05    |   0.0 |  0.00
-Modify  | 0.009278   | 0.0093917  | 0.009528   |   0.1 |  1.04
-Other   |            | 0.006797   |            |       |  0.75
-
-Nlocal:    8000 ave 8018 max 7967 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Nghost:    9131 ave 9164 max 9113 min
-Histogram: 2 0 0 1 0 0 0 0 0 1
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-
-Total # of neighbors = 4253750
-Ave neighs/atom = 132.93
-Neighbor list builds = 3
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/kim/log.22Mar2019.query.g++.1 b/examples/kim/log.22Mar2019.query.g++.1
deleted file mode 100644
index 034bb13bba..0000000000
--- a/examples/kim/log.22Mar2019.query.g++.1
+++ /dev/null
@@ -1,34 +0,0 @@
-LAMMPS (28 Feb 2019)
-
-# example for performing a query to the OpenKIM test database to retrieve
-# a parameter to be used in the input. here it requests the aluminium
-# lattice constant for a specific test used for a specific model and then
-# assigns it to the variable 'latconst'
-
-units metal
-info variables out log
-
-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
-Printed on Fri Mar 22 20:00:56 2019
-
-
-Variable information:
-
-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
-
-kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
-info variables out log
-
-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
-Printed on Fri Mar 22 20:00:57 2019
-
-
-Variable information:
-Variable[  0]: latconst  ,  style = string    ,  def = 4.03208274841
-
-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
-
-lattice fcc ${latconst}
-lattice fcc 4.03208274841
-Lattice spacing in x,y,z = 4.03208 4.03208 4.03208
-Total wall time: 0:00:00
diff --git a/examples/kim/log.7Aug19.in.kim-ex.melt.clang.1 b/examples/kim/log.7Aug19.in.kim-ex.melt.clang.1
new file mode 100644
index 0000000000..17fa1bc534
--- /dev/null
+++ b/examples/kim/log.7Aug19.in.kim-ex.melt.clang.1
@@ -0,0 +1,107 @@
+LAMMPS (7 Aug 2019)
+# 3d Lennard-Jones melt
+#
+# This example requires that the example models provided with
+# the kim-api package are installed.  see the ./lib/kim/README or
+# ./lib/kim/Install.py files for details on how to install these
+# example models.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+kim_init	LennardJones_Ar real
+#=== BEGIN kim-init ==========================================
+units real
+#=== END kim-init ============================================
+
+
+lattice		fcc 4.4300
+Lattice spacing in x,y,z = 4.43 4.43 4.43
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.004321 secs
+
+kim_interactions Ar
+#=== BEGIN kim_interactions ==================================
+pair_style kim LennardJones_Ar
+WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
+WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
+pair_coeff * * Ar 
+#=== END kim_interactions ====================================
+
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.45
+  ghost atom cutoff = 8.45
+  binsize = 4.225, bins = 21 21 21
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair kim, perpetual
+      attributes: full, newton off, cut 8.45
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          200    145069.63            0    164146.22    128015.94 
+     100    95.179703    154939.42            0    164017.94    131602.75 
+Loop time of 3.48256 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 2.481 ns/day, 9.674 hours/ns, 28.715 timesteps/s
+98.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.0502     | 3.0502     | 3.0502     |   0.0 | 87.59
+Neigh   | 0.3646     | 0.3646     | 0.3646     |   0.0 | 10.47
+Comm    | 0.01783    | 0.01783    | 0.01783    |   0.0 |  0.51
+Output  | 6.8e-05    | 6.8e-05    | 6.8e-05    |   0.0 |  0.00
+Modify  | 0.034349   | 0.034349   | 0.034349   |   0.0 |  0.99
+Other   |            | 0.01547    |            |       |  0.44
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19911 ave 19911 max 19911 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4253750
+Ave neighs/atom = 132.93
+Neighbor list builds = 3
+Dangerous builds = 0
+Total wall time: 0:00:03
diff --git a/examples/kim/log.7Aug19.in.kim-ex.melt.clang.4 b/examples/kim/log.7Aug19.in.kim-ex.melt.clang.4
new file mode 100644
index 0000000000..8e076815fc
--- /dev/null
+++ b/examples/kim/log.7Aug19.in.kim-ex.melt.clang.4
@@ -0,0 +1,113 @@
+LAMMPS (7 Aug 2019)
+# 3d Lennard-Jones melt
+#
+# This example requires that the example models provided with
+# the kim-api package are installed.  see the ./lib/kim/README or
+# ./lib/kim/Install.py files for details on how to install these
+# example models.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+kim_init	LennardJones_Ar real
+#=== BEGIN kim-init ==========================================
+units real
+#=== END kim-init ============================================
+
+
+lattice		fcc 4.4300
+Lattice spacing in x,y,z = 4.43 4.43 4.43
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.000989 secs
+
+kim_interactions Ar
+#=== BEGIN kim_interactions ==================================
+pair_style kim LennardJones_Ar
+WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
+WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
+pair_coeff * * Ar 
+WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
+WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
+#=== END kim_interactions ====================================
+
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
+WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
+WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
+WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.45
+  ghost atom cutoff = 8.45
+  binsize = 4.225, bins = 21 21 21
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair kim, perpetual
+      attributes: full, newton off, cut 8.45
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+Per MPI rank memory allocation (min/avg/max) = 9.791 | 9.791 | 9.791 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          200    145069.63            0    164146.22    128015.94 
+     100    95.179703    154939.42            0    164017.94    131602.75 
+Loop time of 0.924494 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 9.346 ns/day, 2.568 hours/ns, 108.167 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.76434    | 0.76847    | 0.77207    |   0.3 | 83.12
+Neigh   | 0.09089    | 0.094446   | 0.099911   |   1.1 | 10.22
+Comm    | 0.038599   | 0.044759   | 0.051381   |   2.1 |  4.84
+Output  | 3.5e-05    | 4e-05      | 4.9e-05    |   0.0 |  0.00
+Modify  | 0.009396   | 0.009685   | 0.009941   |   0.2 |  1.05
+Other   |            | 0.00709    |            |       |  0.77
+
+Nlocal:    8000 ave 8018 max 7967 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost:    9131 ave 9164 max 9113 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+
+Total # of neighbors = 4253750
+Ave neighs/atom = 132.93
+Neighbor list builds = 3
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1 b/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1
new file mode 100644
index 0000000000..1ca44c98ef
--- /dev/null
+++ b/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1
@@ -0,0 +1,124 @@
+LAMMPS (7 Aug 2019)
+# 3d Lennard-Jones melt
+#
+# This example requires that the KIM Portable Model (PM)
+# SW_StillingerWeber_1985_Si__MO_405512056662_005
+# is installed.  This can be done with the command
+#   kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
+# If this command does not work, you may need to setup your PATH to find the utility.
+# If you installed the kim-api using the LAMMPS CMake build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS build directory)
+#   source ./kim_build-prefix/bin/kim-api-activate
+# If you installed the kim-api using the LAMMPS Make build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS src directory)
+#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
+# (where you should relplace X.Y.Z with the appropriate kim-api version number).
+#
+# Or, see https://openkim.org/doc/obtaining-models for alternative options.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+kim_init	SW_StillingerWeber_1985_Si__MO_405512056662_005 real
+#=== BEGIN kim-init ==========================================
+units real
+#=== END kim-init ============================================
+
+kim_query       a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
+#=== BEGIN kim-query =========================================
+variable a0 string 4.146581932902336
+#=== END kim-query ===========================================
+
+
+lattice		fcc ${a0}
+lattice		fcc 4.146581932902336
+Lattice spacing in x,y,z = 4.14658 4.14658 4.14658
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (82.9316 82.9316 82.9316)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.005415 secs
+
+kim_interactions Si
+#=== BEGIN kim_interactions ==================================
+pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
+pair_coeff * * Si 
+#=== END kim_interactions ====================================
+
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.07118
+  ghost atom cutoff = 4.07118
+  binsize = 2.03559, bins = 41 41 41
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair kim, perpetual
+      attributes: full, newton off, cut 4.07118
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+Per MPI rank memory allocation (min/avg/max) = 10.36 | 10.36 | 10.36 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          200   -126084.25            0   -107007.66    1528.8768 
+     100    94.450495   -116016.03            0   -107007.07    2282.2685 
+Loop time of 74.6055 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 0.116 ns/day, 207.238 hours/ns, 1.340 timesteps/s
+98.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 74.446     | 74.446     | 74.446     |   0.0 | 99.79
+Neigh   | 0.096611   | 0.096611   | 0.096611   |   0.0 |  0.13
+Comm    | 0.014594   | 0.014594   | 0.014594   |   0.0 |  0.02
+Output  | 7.9e-05    | 7.9e-05    | 7.9e-05    |   0.0 |  0.00
+Modify  | 0.03454    | 0.03454    | 0.03454    |   0.0 |  0.05
+Other   |            | 0.01396    |            |       |  0.02
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    9667 ave 9667 max 9667 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  450192 ave 450192 max 450192 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 450192
+Ave neighs/atom = 14.0685
+Neighbor list builds = 3
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:16
diff --git a/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4 b/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4
new file mode 100644
index 0000000000..8c4148ce15
--- /dev/null
+++ b/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4
@@ -0,0 +1,124 @@
+LAMMPS (7 Aug 2019)
+# 3d Lennard-Jones melt
+#
+# This example requires that the KIM Portable Model (PM)
+# SW_StillingerWeber_1985_Si__MO_405512056662_005
+# is installed.  This can be done with the command
+#   kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
+# If this command does not work, you may need to setup your PATH to find the utility.
+# If you installed the kim-api using the LAMMPS CMake build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS build directory)
+#   source ./kim_build-prefix/bin/kim-api-activate
+# If you installed the kim-api using the LAMMPS Make build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS src directory)
+#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
+# (where you should relplace X.Y.Z with the appropriate kim-api version number).
+#
+# Or, see https://openkim.org/doc/obtaining-models for alternative options.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+kim_init	SW_StillingerWeber_1985_Si__MO_405512056662_005 real
+#=== BEGIN kim-init ==========================================
+units real
+#=== END kim-init ============================================
+
+kim_query       a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
+#=== BEGIN kim-query =========================================
+variable a0 string 4.146581932902336
+#=== END kim-query ===========================================
+
+
+lattice		fcc ${a0}
+lattice		fcc 4.146581932902336
+Lattice spacing in x,y,z = 4.14658 4.14658 4.14658
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (82.9316 82.9316 82.9316)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.000946 secs
+
+kim_interactions Si
+#=== BEGIN kim_interactions ==================================
+pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
+pair_coeff * * Si 
+#=== END kim_interactions ====================================
+
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.07118
+  ghost atom cutoff = 4.07118
+  binsize = 2.03559, bins = 41 41 41
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair kim, perpetual
+      attributes: full, newton off, cut 4.07118
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+Per MPI rank memory allocation (min/avg/max) = 3.489 | 3.489 | 3.489 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          200   -126084.25            0   -107007.66    1528.8768 
+     100    94.450495   -116016.03            0   -107007.07    2282.2685 
+Loop time of 19.0792 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 0.453 ns/day, 52.998 hours/ns, 5.241 timesteps/s
+99.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 18.78      | 18.855     | 18.937     |   1.5 | 98.83
+Neigh   | 0.026047   | 0.026274   | 0.0266     |   0.1 |  0.14
+Comm    | 0.09039    | 0.17196    | 0.24675    |  15.9 |  0.90
+Output  | 3.9e-05    | 4.975e-05  | 6.1e-05    |   0.0 |  0.00
+Modify  | 0.015667   | 0.015819   | 0.016008   |   0.1 |  0.08
+Other   |            | 0.01008    |            |       |  0.05
+
+Nlocal:    8000 ave 8029 max 7968 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost:    4259 ave 4303 max 4202 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  112548 ave 113091 max 111995 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+
+Total # of neighbors = 450192
+Ave neighs/atom = 14.0685
+Neighbor list builds = 3
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:20
diff --git a/examples/kim/log.7Aug19.in.kim-pm.melt.clang.1 b/examples/kim/log.7Aug19.in.kim-pm.melt.clang.1
new file mode 100644
index 0000000000..f5845d7fc4
--- /dev/null
+++ b/examples/kim/log.7Aug19.in.kim-pm.melt.clang.1
@@ -0,0 +1,118 @@
+LAMMPS (7 Aug 2019)
+# 3d Lennard-Jones melt
+#
+# This example requires that the KIM Portable Model (PM)
+# SW_StillingerWeber_1985_Si__MO_405512056662_005
+# is installed.  This can be done with the command
+#   kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
+# If this command does not work, you may need to setup your PATH to find the utility.
+# If you installed the kim-api using the LAMMPS CMake build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS build directory)
+#   source ./kim_build-prefix/bin/kim-api-activate
+# If you installed the kim-api using the LAMMPS Make build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS src directory)
+#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
+# (where you should relplace X.Y.Z with the appropriate kim-api version number).
+#
+# Or, see https://openkim.org/doc/obtaining-models for alternative options.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+kim_init	SW_StillingerWeber_1985_Si__MO_405512056662_005 real
+#=== BEGIN kim-init ==========================================
+units real
+#=== END kim-init ============================================
+
+
+lattice		fcc 4.4300
+Lattice spacing in x,y,z = 4.43 4.43 4.43
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.003591 secs
+
+kim_interactions Si
+#=== BEGIN kim_interactions ==================================
+pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
+pair_coeff * * Si 
+#=== END kim_interactions ====================================
+
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.07118
+  ghost atom cutoff = 4.07118
+  binsize = 2.03559, bins = 44 44 44
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair kim, perpetual
+      attributes: full, newton off, cut 4.07118
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          200   -85249.847            0   -66173.259   -33302.387 
+     100    253.43357    -90346.68            0   -66173.441   -14888.698 
+Loop time of 74.248 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 0.116 ns/day, 206.244 hours/ns, 1.347 timesteps/s
+98.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 74.118     | 74.118     | 74.118     |   0.0 | 99.83
+Neigh   | 0.069623   | 0.069623   | 0.069623   |   0.0 |  0.09
+Comm    | 0.0137     | 0.0137     | 0.0137     |   0.0 |  0.02
+Output  | 7.6e-05    | 7.6e-05    | 7.6e-05    |   0.0 |  0.00
+Modify  | 0.031883   | 0.031883   | 0.031883   |   0.0 |  0.04
+Other   |            | 0.01433    |            |       |  0.02
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7760 ave 7760 max 7760 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  402352 ave 402352 max 402352 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 402352
+Ave neighs/atom = 12.5735
+Neighbor list builds = 4
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:14
diff --git a/examples/kim/log.7Aug19.in.kim-pm.melt.clang.4 b/examples/kim/log.7Aug19.in.kim-pm.melt.clang.4
new file mode 100644
index 0000000000..0b4632b999
--- /dev/null
+++ b/examples/kim/log.7Aug19.in.kim-pm.melt.clang.4
@@ -0,0 +1,118 @@
+LAMMPS (7 Aug 2019)
+# 3d Lennard-Jones melt
+#
+# This example requires that the KIM Portable Model (PM)
+# SW_StillingerWeber_1985_Si__MO_405512056662_005
+# is installed.  This can be done with the command
+#   kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
+# If this command does not work, you may need to setup your PATH to find the utility.
+# If you installed the kim-api using the LAMMPS CMake build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS build directory)
+#   source ./kim_build-prefix/bin/kim-api-activate
+# If you installed the kim-api using the LAMMPS Make build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS src directory)
+#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
+# (where you should relplace X.Y.Z with the appropriate kim-api version number).
+#
+# Or, see https://openkim.org/doc/obtaining-models for alternative options.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+kim_init	SW_StillingerWeber_1985_Si__MO_405512056662_005 real
+#=== BEGIN kim-init ==========================================
+units real
+#=== END kim-init ============================================
+
+
+lattice		fcc 4.4300
+Lattice spacing in x,y,z = 4.43 4.43 4.43
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.000997 secs
+
+kim_interactions Si
+#=== BEGIN kim_interactions ==================================
+pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
+pair_coeff * * Si 
+#=== END kim_interactions ====================================
+
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.07118
+  ghost atom cutoff = 4.07118
+  binsize = 2.03559, bins = 44 44 44
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair kim, perpetual
+      attributes: full, newton off, cut 4.07118
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+Per MPI rank memory allocation (min/avg/max) = 3.517 | 3.517 | 3.517 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          200   -85249.847            0   -66173.259   -33302.387 
+     100    253.43357    -90346.68            0   -66173.441   -14888.698 
+Loop time of 19.0287 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 0.454 ns/day, 52.857 hours/ns, 5.255 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 18.81      | 18.838     | 18.883     |   0.6 | 99.00
+Neigh   | 0.018598   | 0.01914    | 0.020732   |   0.7 |  0.10
+Comm    | 0.10341    | 0.1475     | 0.17393    |   7.1 |  0.78
+Output  | 6e-05      | 6.225e-05  | 6.7e-05    |   0.0 |  0.00
+Modify  | 0.014839   | 0.014925   | 0.015047   |   0.1 |  0.08
+Other   |            | 0.008997   |            |       |  0.05
+
+Nlocal:    8000 ave 8014 max 7988 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Nghost:    3374.75 ave 3389 max 3361 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  100588 ave 100856 max 100392 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+
+Total # of neighbors = 402352
+Ave neighs/atom = 12.5735
+Neighbor list builds = 4
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:19
diff --git a/examples/kim/log.7Aug19.in.kim-sm.melt.clang.1 b/examples/kim/log.7Aug19.in.kim-sm.melt.clang.1
new file mode 100644
index 0000000000..1b77e58a3a
--- /dev/null
+++ b/examples/kim/log.7Aug19.in.kim-sm.melt.clang.1
@@ -0,0 +1,71 @@
+LAMMPS (7 Aug 2019)
+# 3d Lennard-Jones melt
+#
+# This example requires that the KIM Simulator Model (PM)
+# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
+# is installed.  This can be done with the command
+#   kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
+# If this command does not work, you may need to setup your PATH to find the utility.
+# If you installed the kim-api using the LAMMPS CMake build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS build directory)
+#   source ./kim_build-prefix/bin/kim-api-activate
+# If you installed the kim-api using the LAMMPS Make build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS src directory)
+#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
+# (where you should relplace X.Y.Z with the appropriate kim-api version number).
+#
+# See https://openkim.org/doc/obtaining-models for alternative options.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+kim_init	Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
+#=== BEGIN kim-init ==========================================
+# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
+# For Simulator             : LAMMPS 28 Feb 2019
+# Running on                : LAMMPS 7 Aug 2019
+#
+units real
+atom_style charge
+neigh_modify one 4000
+#=== END kim-init ============================================
+
+
+lattice		fcc 4.4300
+Lattice spacing in x,y,z = 4.43 4.43 4.43
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.003447 secs
+
+kim_interactions O
+#=== BEGIN kim_interactions ==================================
+pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6Acs1QDbXgBx/lmp_control safezone 2.0 mincap 100
+ERROR: Unrecognized pair style 'reax/c' is part of the USER-REAXC package which is not enabled in this LAMMPS binary. (../force.cpp:262)
+Last command: pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6Acs1QDbXgBx/lmp_control safezone 2.0 mincap 100
+--------------------------------------------------------------------------
+Primary job  terminated normally, but 1 process returned
+a non-zero exit code. Per user-direction, the job has been aborted.
+--------------------------------------------------------------------------
+--------------------------------------------------------------------------
+mpirun detected that one or more processes exited with non-zero status, thus causing
+the job to be terminated. The first process to do so was:
+
+  Process name: [[33054,1],0]
+  Exit code:    1
+--------------------------------------------------------------------------
diff --git a/examples/kim/log.7Aug19.in.kim-sm.melt.clang.4 b/examples/kim/log.7Aug19.in.kim-sm.melt.clang.4
new file mode 100644
index 0000000000..72b62beffb
--- /dev/null
+++ b/examples/kim/log.7Aug19.in.kim-sm.melt.clang.4
@@ -0,0 +1,60 @@
+LAMMPS (7 Aug 2019)
+# 3d Lennard-Jones melt
+#
+# This example requires that the KIM Simulator Model (PM)
+# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
+# is installed.  This can be done with the command
+#   kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
+# If this command does not work, you may need to setup your PATH to find the utility.
+# If you installed the kim-api using the LAMMPS CMake build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS build directory)
+#   source ./kim_build-prefix/bin/kim-api-activate
+# If you installed the kim-api using the LAMMPS Make build, you can do the following
+# (where the current working directory is assumed to be the LAMMPS src directory)
+#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
+# (where you should relplace X.Y.Z with the appropriate kim-api version number).
+#
+# See https://openkim.org/doc/obtaining-models for alternative options.
+#
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+kim_init	Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
+#=== BEGIN kim-init ==========================================
+# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
+# For Simulator             : LAMMPS 28 Feb 2019
+# Running on                : LAMMPS 7 Aug 2019
+#
+units real
+atom_style charge
+neigh_modify one 4000
+#=== END kim-init ============================================
+
+
+lattice		fcc 4.4300
+Lattice spacing in x,y,z = 4.43 4.43 4.43
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.001307 secs
+
+kim_interactions O
+#=== BEGIN kim_interactions ==================================
+pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100
+ERROR: Unrecognized pair style 'reax/c' is part of the USER-REAXC package which is not enabled in this LAMMPS binary. (../force.cpp:262)
+Last command: pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100
diff --git a/examples/kim/log.7Aug19.in.lammps.melt.clang.1 b/examples/kim/log.7Aug19.in.lammps.melt.clang.1
new file mode 100644
index 0000000000..f697504777
--- /dev/null
+++ b/examples/kim/log.7Aug19.in.lammps.melt.clang.1
@@ -0,0 +1,92 @@
+LAMMPS (7 Aug 2019)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		real
+
+lattice		fcc 4.4300
+Lattice spacing in x,y,z = 4.43 4.43 4.43
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.003037 secs
+
+pair_style	lj/cut 8.1500
+pair_coeff	1 1 0.0104 3.4000
+
+#pair_style      kim LennardJones_Ar
+#pair_coeff      * * Ar
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.45
+  ghost atom cutoff = 8.45
+  binsize = 4.225, bins = 21 21 21
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          200    6290.8194            0    25367.408    6750.7421 
+     100    98.747096    15900.676            0    25319.465    10184.453 
+Loop time of 2.43768 on 1 procs for 100 steps with 32000 atoms
+
+Performance: 3.544 ns/day, 6.771 hours/ns, 41.023 timesteps/s
+97.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.1895     | 2.1895     | 2.1895     |   0.0 | 89.82
+Neigh   | 0.17546    | 0.17546    | 0.17546    |   0.0 |  7.20
+Comm    | 0.021001   | 0.021001   | 0.021001   |   0.0 |  0.86
+Output  | 7.9e-05    | 7.9e-05    | 7.9e-05    |   0.0 |  0.00
+Modify  | 0.034253   | 0.034253   | 0.034253   |   0.0 |  1.41
+Other   |            | 0.01735    |            |       |  0.71
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19911 ave 19911 max 19911 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.96027e+06 ave 1.96027e+06 max 1.96027e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1960266
+Ave neighs/atom = 61.2583
+Neighbor list builds = 3
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/kim/log.7Aug19.in.lammps.melt.clang.4 b/examples/kim/log.7Aug19.in.lammps.melt.clang.4
new file mode 100644
index 0000000000..2d25348b06
--- /dev/null
+++ b/examples/kim/log.7Aug19.in.lammps.melt.clang.4
@@ -0,0 +1,92 @@
+LAMMPS (7 Aug 2019)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		real
+
+lattice		fcc 4.4300
+Lattice spacing in x,y,z = 4.43 4.43 4.43
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.001194 secs
+
+pair_style	lj/cut 8.1500
+pair_coeff	1 1 0.0104 3.4000
+
+#pair_style      kim LennardJones_Ar
+#pair_coeff      * * Ar
+
+mass		1 39.95
+velocity	all create 200.0 232345 loop geom
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+#fix		1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
+
+run 		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.45
+  ghost atom cutoff = 8.45
+  binsize = 4.225, bins = 21 21 21
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+Per MPI rank memory allocation (min/avg/max) = 7.633 | 7.633 | 7.633 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          200    6290.8194            0    25367.408    6750.7421 
+     100    98.747096    15900.676            0    25319.465    10184.453 
+Loop time of 0.726239 on 4 procs for 100 steps with 32000 atoms
+
+Performance: 11.897 ns/day, 2.017 hours/ns, 137.696 timesteps/s
+98.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.57617    | 0.5835     | 0.59084    |   0.9 | 80.34
+Neigh   | 0.046682   | 0.047783   | 0.048641   |   0.3 |  6.58
+Comm    | 0.065469   | 0.071509   | 0.07899    |   2.3 |  9.85
+Output  | 3.9e-05    | 4.6e-05    | 6.1e-05    |   0.0 |  0.01
+Modify  | 0.013205   | 0.01363    | 0.014044   |   0.3 |  1.88
+Other   |            | 0.009775   |            |       |  1.35
+
+Nlocal:    8000 ave 8012 max 7989 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+Nghost:    9131 ave 9142 max 9119 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:    490066 ave 491443 max 489273 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 1960266
+Ave neighs/atom = 61.2583
+Neighbor list builds = 3
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/steinhardt/in.bcc b/examples/steinhardt/in.bcc
new file mode 100644
index 0000000000..a0348fdcd9
--- /dev/null
+++ b/examples/steinhardt/in.bcc
@@ -0,0 +1,91 @@
+# Steinhardt-Nelson bond orientational order parameters for BCC
+
+variable  	rcut equal 3.0
+
+boundary	p p p
+
+atom_style	atomic
+neighbor	0.3 bin
+neigh_modify	delay 5
+
+# create geometry
+
+lattice		bcc 1.0
+region		box block 0 3 0 3 0 3
+create_box	1 box
+create_atoms	1 box
+
+mass		1 1.0
+
+# LJ potentials
+
+pair_style	lj/cut ${rcut}
+pair_coeff	* * 1.0 1.0 ${rcut}
+
+# 14 neighbors, perfect crystal 
+
+compute 	qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes
+compute 	avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] c_qlwlhat[6] 
+compute 	avwlhat all reduce ave c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] c_qlwlhat[11] c_qlwlhat[12] 
+
+thermo_style    custom step temp epair etotal c_avql[*] c_avwlhat[*]
+
+run		0
+
+# check Q_l values
+
+print " "
+print "*******************************************************************"
+print " "
+print "Comparison with reference values of Q_l "
+print "   [Table I in W. Mickel, S. C. Kapfer," 
+print "   G. E. Schroeder-Turkand, K. Mecke, "
+print "   J. Chem. Phys. 138, 044501 (2013).]"
+print " "
+
+variable 	q2ref equal 0.0
+variable 	q4ref equal 0.036
+variable 	q6ref equal 0.511
+variable 	q8ref equal 0.429
+variable 	q10ref equal 0.195
+variable 	q12ref equal 0.405
+
+variable 	q2 equal c_avql[1]
+variable 	q4 equal c_avql[2]
+variable 	q6 equal c_avql[3]
+variable 	q8 equal c_avql[4]
+variable 	q10 equal c_avql[5]
+variable 	q12 equal c_avql[6]
+
+print "q2     = $(v_q2:%10.6f) delta = $(v_q2-v_q2ref:%10.4f)"
+print "q4     = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)"
+print "q6     = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)"
+print "q8     = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)"
+print "q10    = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)"
+print "q12    = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)"
+
+# check W_l_hat values
+
+print " "
+print "Comparison with reference values of W_l_hat"
+print "   [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, "
+print "   Phys. Rev. B 28, 784 (1983).]"
+print " "
+
+variable 	w4hatref equal 0.159317
+variable 	w6hatref equal 0.013161
+variable 	w8hatref equal -0.058455
+variable 	w10hatref equal -0.090130
+
+variable 	w4hat equal c_avwlhat[2]
+variable 	w6hat equal c_avwlhat[3]
+variable 	w8hat equal c_avwlhat[4]
+variable 	w10hat equal c_avwlhat[5]
+
+print "w4hat  = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)"
+print "w6hat  = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)"
+print "w8hat  = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)"
+print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)"
+print " "
+print "*******************************************************************"
+print " "
diff --git a/examples/steinhardt/in.fcc b/examples/steinhardt/in.fcc
new file mode 100644
index 0000000000..6d2775d0bb
--- /dev/null
+++ b/examples/steinhardt/in.fcc
@@ -0,0 +1,88 @@
+# Steinhardt-Nelson bond orientational order parameters for FCC
+
+variable  	rcut equal 3.0
+
+boundary	p p p
+
+atom_style	atomic
+neighbor	0.3 bin
+neigh_modify	delay 5
+
+# create geometry
+
+lattice		fcc 1.0
+region		box block 0 3 0 3 0 3
+create_box	1 box
+create_atoms	1 box
+
+mass		1 1.0
+
+# LJ potentials
+
+pair_style	lj/cut ${rcut}
+pair_coeff	* * 1.0 1.0 ${rcut}
+
+# 12 neighbors, perfect crystal
+
+compute 	qlwlhat all orientorder/atom wl/hat yes
+compute 	avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] 
+compute 	avwlhat all reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10]
+
+thermo_style    custom step temp epair etotal c_avql[*] c_avwlhat[*]
+
+run		0
+
+# check Q_l values
+
+print " "
+print "*******************************************************************"
+print " "
+print "Comparison with reference values of Q_l "
+print "   [Table I in W. Mickel, S. C. Kapfer," 
+print "   G. E. Schroeder-Turkand, K. Mecke, "
+print "   J. Chem. Phys. 138, 044501 (2013).]"
+print " "
+
+variable 	q4ref equal 0.190
+variable 	q6ref equal 0.575
+variable 	q8ref equal 0.404
+variable 	q10ref equal 0.013
+variable 	q12ref equal 0.600
+
+variable 	q4 equal c_avql[1]
+variable 	q6 equal c_avql[2]
+variable 	q8 equal c_avql[3]
+variable 	q10 equal c_avql[4]
+variable 	q12 equal c_avql[5]
+
+print "q4     = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)"
+print "q6     = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)"
+print "q8     = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)"
+print "q10    = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)"
+print "q12    = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)"
+
+# check W_l_hat values
+
+print " "
+print "Comparison with reference values of W_l_hat"
+print "   [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, "
+print "   Phys. Rev. B 28, 784 (1983).]"
+print " "
+
+variable 	w4hatref equal -0.159316
+variable 	w6hatref equal -0.013161
+variable 	w8hatref equal 0.058454
+variable 	w10hatref equal -0.090128
+
+variable 	w4hat equal c_avwlhat[1]
+variable 	w6hat equal c_avwlhat[2]
+variable 	w8hat equal c_avwlhat[3]
+variable 	w10hat equal c_avwlhat[4]
+
+print "w4hat  = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)"
+print "w6hat  = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)"
+print "w8hat  = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)"
+print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)"
+print " "
+print "*******************************************************************"
+print " "
diff --git a/examples/steinhardt/in.icos b/examples/steinhardt/in.icos
new file mode 100644
index 0000000000..d0d61a902d
--- /dev/null
+++ b/examples/steinhardt/in.icos
@@ -0,0 +1,106 @@
+# Steinhardt-Nelson bond orientational order parameters for icosahedral cluster
+# W_6_hat is sensitive to icosohedral order
+
+variable        rcut equal 1.2 # a bit bigger than LJ Rmin 
+variable        rcutred equal 0.75 # a bit bigger than 1/sqrt(2)
+
+# create a perfect fcc crystallite
+
+atom_style	atomic
+boundary	s s s
+lattice		fcc 1.0 # neighbors at LJ Rmin
+region		box block 0 2 0 2 0 2
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+region 		centralatom sphere 1 1 1 0.0 side in
+group 		centralatom region centralatom
+
+region 		mysphere sphere 1 1 1 ${rcutred} side out
+delete_atoms 	region mysphere
+
+# LJ potential
+
+pair_style	lj/cut 100.0
+pair_coeff	* * 1.0 1.0 100.0
+
+# define output for central atom
+
+compute 	qlwlhat all orientorder/atom wl/hat yes cutoff ${rcut} nnn NULL
+compute 	avql centralatom reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] 
+compute 	avwlhat centralatom reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] 
+variable	q6 equal c_avql[2]
+variable	w6hat equal c_avwlhat[2]
+
+compute 	mype all pe/atom
+compute 	centralatompe centralatom reduce ave c_mype
+
+# gently equilibrate the crystallite
+
+velocity     	all create 0.001 482748
+fix	     	1 all nve
+neighbor	0.3 bin
+neigh_modify	every 1 check no delay 0
+timestep	0.003
+thermo_style    custom step temp epair etotal c_centralatompe v_q6 v_w6hat
+thermo		10
+
+run		10
+
+# quench to icosehedral cluster
+
+minimize      	1.0e-10 1.0e-6 100 1000
+
+# check Q_l values
+
+print " "
+print "*******************************************************************"
+print " "
+print "Comparison with reference values of Q_l "
+print "   [Table I in W. Mickel, S. C. Kapfer," 
+print "   G. E. Schroeder-Turkand, K. Mecke, "
+print "   J. Chem. Phys. 138, 044501 (2013).]"
+print " "
+
+variable 	q4ref equal 0.0
+variable 	q6ref equal 0.663
+variable 	q8ref equal 0.0
+variable 	q10ref equal 0.363
+variable 	q12ref equal 0.585
+
+variable 	q4 equal c_avql[1]
+variable 	q6 equal c_avql[2]
+variable 	q8 equal c_avql[3]
+variable 	q10 equal c_avql[4]
+variable 	q12 equal c_avql[5]
+
+print "q4     = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)"
+print "q6     = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)"
+print "q8     = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)"
+print "q10    = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)"
+print "q12    = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)"
+
+# check W_l_hat values
+
+print " "
+print "Comparison with reference values of W_l_hat"
+print "   [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, "
+print "   Phys. Rev. B 28, 784 (1983).]"
+print " "
+
+variable 	w6hatref equal -0.169754
+variable 	w10hatref equal -0.093967
+
+variable 	w4hat equal c_avwlhat[1]
+variable 	w6hat equal c_avwlhat[2]
+variable 	w8hat equal c_avwlhat[3]
+variable 	w10hat equal c_avwlhat[4]
+variable 	w12hat equal c_avwlhat[5]
+
+print "w6hat  = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)"
+print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)"
+print " "
+print "*******************************************************************"
+print " "
+
diff --git a/lib/colvars/Makefile.common b/lib/colvars/Makefile.common
index e3fa4662e6..5958765077 100644
--- a/lib/colvars/Makefile.common
+++ b/lib/colvars/Makefile.common
@@ -34,6 +34,7 @@ COLVARS_SRCS = \
         colvarcomp_coordnums.cpp \
         colvarcomp.cpp \
         colvarcomp_distances.cpp \
+        colvarcomp_gpath.cpp \
         colvarcomp_protein.cpp \
         colvarcomp_rotations.cpp \
         colvar.cpp \
diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp
index 723a54ad39..e3676084ac 100644
--- a/lib/colvars/colvar.cpp
+++ b/lib/colvars/colvar.cpp
@@ -791,6 +791,11 @@ int colvar::init_components(std::string const &conf)
     "inertia", "inertia");
   error_code |= init_components_type<inertia_z>(conf, "moment of inertia around an axis", "inertiaZ");
   error_code |= init_components_type<eigenvector>(conf, "eigenvector", "eigenvector");
+  error_code |= init_components_type<gspath>(conf, "geometrical path collective variables (s)", "gspath");
+  error_code |= init_components_type<gzpath>(conf, "geometrical path collective variables (z)", "gzpath");
+  error_code |= init_components_type<linearCombination>(conf, "linear combination of other collective variables", "subColvar");
+  error_code |= init_components_type<gspathCV>(conf, "geometrical path collective variables (s) for other CVs", "gspathCV");
+  error_code |= init_components_type<gzpathCV>(conf, "geometrical path collective variables (z) for other CVs", "gzpathCV");
 
   if (!cvcs.size() || (error_code != COLVARS_OK)) {
     cvm::error("Error: no valid components were provided "
@@ -1495,6 +1500,8 @@ int colvar::calc_colvar_properties()
     // calculate the velocity by finite differences
     if (cvm::step_relative() == 0) {
       x_old = x;
+      v_fdiff.reset(); // Do not pretend we know anything about the actual velocity
+      // eg. upon restarting. That would require saving v_fdiff or x_old to the state file
     } else {
       v_fdiff = fdiff_velocity(x_old, x);
       v_reported = v_fdiff;
@@ -1516,8 +1523,9 @@ int colvar::calc_colvar_properties()
       x_ext = prev_x_ext;
       v_ext = prev_v_ext;
     }
-
     // report the restraint center as "value"
+    // These position and velocities come from integration at the _previous timestep_ in update_forces_energy()
+    // But we report values at the beginning of the timestep (value at t=0 on the first timestep)
     x_reported = x_ext;
     v_reported = v_ext;
     // the "total force" with the extended Lagrangian is
@@ -1651,8 +1659,6 @@ cvm::real colvar::update_forces_energy()
       // is equal to the actual coordinate
       x_ext = x;
     }
-    // Report extended value
-    x_reported = x_ext;
   }
 
   // Now adding the force on the actual colvar (for those biases that
@@ -1975,9 +1981,8 @@ std::istream & colvar::read_restart(std::istream &is)
   }
 
   if (is_enabled(f_cv_extended_Lagrangian)) {
-
     if ( !(get_keyval(conf, "extended_x", x_ext,
-                      colvarvalue(x.type()), colvarparse::parse_silent)) &&
+                      colvarvalue(x.type()), colvarparse::parse_silent)) ||
          !(get_keyval(conf, "extended_v", v_ext,
                       colvarvalue(x.type()), colvarparse::parse_silent)) ) {
       cvm::log("Error: restart file does not contain "
@@ -2079,11 +2084,11 @@ std::ostream & colvar::write_restart(std::ostream &os) {
     os << "  extended_x "
        << std::setprecision(cvm::cv_prec)
        << std::setw(cvm::cv_width)
-       << x_ext << "\n"
+       << x_reported << "\n"
        << "  extended_v "
        << std::setprecision(cvm::cv_prec)
        << std::setw(cvm::cv_width)
-       << v_ext << "\n";
+       << v_reported << "\n";
   }
 
   os << "}\n\n";
@@ -2150,7 +2155,6 @@ std::ostream & colvar::write_traj_label(std::ostream & os)
 std::ostream & colvar::write_traj(std::ostream &os)
 {
   os << " ";
-
   if (is_enabled(f_cv_output_value)) {
 
     if (is_enabled(f_cv_extended_Lagrangian)) {
diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h
index 74f7fdee51..e2ab0f3c1d 100644
--- a/lib/colvars/colvar.h
+++ b/lib/colvars/colvar.h
@@ -569,6 +569,14 @@ public:
   class alpha_dihedrals;
   class alpha_angles;
   class dihedPC;
+  class componentDisabled;
+  class CartesianBasedPath;
+  class gspath;
+  class gzpath;
+  class linearCombination;
+  class CVBasedPath;
+  class gspathCV;
+  class gzpathCV;
 
   // non-scalar components
   class distance_vec;
diff --git a/lib/colvars/colvar_geometricpath.h b/lib/colvars/colvar_geometricpath.h
new file mode 100644
index 0000000000..a7ef7f337c
--- /dev/null
+++ b/lib/colvars/colvar_geometricpath.h
@@ -0,0 +1,270 @@
+#ifndef GEOMETRICPATHCV_H
+#define GEOMETRICPATHCV_H
+// This file is part of the Collective Variables module (Colvars).
+// The original version of Colvars and its updates are located at:
+// https://github.com/colvars/colvars
+// Please update all Colvars source files before making any changes.
+// If you wish to distribute your changes, please submit them to the
+// Colvars repository at GitHub.
+
+
+#include <vector>
+#include <cmath>
+#include <iostream>
+#include <algorithm>
+#include <string>
+#include <map>
+
+namespace GeometricPathCV {
+
+enum path_sz {S, Z};
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+class GeometricPathBase {
+private:
+    struct doCompareFrameDistance {
+        doCompareFrameDistance(const GeometricPathBase& obj): m_obj(obj) {}
+        const GeometricPathBase& m_obj;
+        bool operator()(const size_t& i1, const size_t& i2) {
+            return m_obj.frame_distances[i1] < m_obj.frame_distances[i2];
+        }
+    };
+protected:
+    scalar_type v1v1;
+    scalar_type v2v2;
+    scalar_type v3v3;
+    scalar_type v4v4;
+    scalar_type v1v3;
+    scalar_type v1v4;
+    scalar_type f;
+    scalar_type dx;
+    scalar_type s;
+    scalar_type z;
+    scalar_type zz;
+    std::vector<element_type> v1;
+    std::vector<element_type> v2;
+    std::vector<element_type> v3;
+    std::vector<element_type> v4;
+    std::vector<element_type> dfdv1;
+    std::vector<element_type> dfdv2;
+    std::vector<element_type> dzdv1;
+    std::vector<element_type> dzdv2;
+    std::vector<scalar_type> frame_distances;
+    std::vector<size_t> frame_index;
+    bool use_second_closest_frame;
+    bool use_third_closest_frame;
+    bool use_z_square;
+    long min_frame_index_1;
+    long min_frame_index_2;
+    long min_frame_index_3;
+    long sign;
+    double M;
+    double m;
+public:
+    GeometricPathBase(size_t vector_size, const element_type& element = element_type(), size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
+    GeometricPathBase(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
+    GeometricPathBase() {}
+    virtual ~GeometricPathBase() {}
+    virtual void initialize(size_t vector_size, const element_type& element = element_type(), size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
+    virtual void initialize(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
+    virtual void prepareVectors();
+    virtual void updateReferenceDistances();
+    virtual void compute();
+    virtual void determineClosestFrames();
+    virtual void computeValue();
+    virtual void computeDerivatives();
+};
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+GeometricPathBase<element_type, scalar_type, path_type>::GeometricPathBase(size_t vector_size, const element_type& element, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
+    initialize(vector_size, element, total_frames, p_use_second_closest_frame, p_use_third_closest_frame, p_use_z_square);
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+GeometricPathBase<element_type, scalar_type, path_type>::GeometricPathBase(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
+    initialize(vector_size, elements, total_frames, p_use_second_closest_frame, p_use_third_closest_frame, p_use_z_square);
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::initialize(size_t vector_size, const element_type& element, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
+    v1v1 = scalar_type();
+    v2v2 = scalar_type();
+    v3v3 = scalar_type();
+    v4v4 = scalar_type();
+    v1v3 = scalar_type();
+    v1v4 = scalar_type();
+    f = scalar_type();
+    dx = scalar_type();
+    z = scalar_type();
+    zz = scalar_type();
+    sign = 0;
+    v1.resize(vector_size, element);
+    v2.resize(vector_size, element);
+    v3.resize(vector_size, element);
+    v4.resize(vector_size, element);
+    dfdv1.resize(vector_size, element);
+    dfdv2.resize(vector_size, element);
+    dzdv1.resize(vector_size, element);
+    dzdv2.resize(vector_size, element);
+    frame_distances.resize(total_frames);
+    frame_index.resize(total_frames);
+    for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) {
+        frame_index[i_frame] = i_frame;
+    }
+    use_second_closest_frame = p_use_second_closest_frame;
+    use_third_closest_frame = p_use_third_closest_frame;
+    use_z_square = p_use_z_square;
+    M = static_cast<scalar_type>(total_frames - 1);
+    m = static_cast<scalar_type>(1.0);
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::initialize(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
+    v1v1 = scalar_type();
+    v2v2 = scalar_type();
+    v3v3 = scalar_type();
+    v4v4 = scalar_type();
+    v1v3 = scalar_type();
+    v1v4 = scalar_type();
+    f = scalar_type();
+    dx = scalar_type();
+    z = scalar_type();
+    zz = scalar_type();
+    sign = 0;
+    v1 = elements;
+    v2 = elements;
+    v3 = elements;
+    v4 = elements;
+    dfdv1 = elements;
+    dfdv2 = elements;
+    dzdv1 = elements;
+    dzdv2 = elements;
+    frame_distances.resize(total_frames);
+    frame_index.resize(total_frames);
+    for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) {
+        frame_index[i_frame] = i_frame;
+    }
+    use_second_closest_frame = p_use_second_closest_frame;
+    use_third_closest_frame = p_use_third_closest_frame;
+    use_z_square = p_use_z_square;
+    M = static_cast<scalar_type>(total_frames - 1);
+    m = static_cast<scalar_type>(1.0);
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::prepareVectors() {
+    std::cout << "Warning: you should not call the prepareVectors() in base class!\n";
+    std::cout << std::flush;
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::updateReferenceDistances() {
+    std::cout << "Warning: you should not call the updateReferenceDistances() in base class!\n";
+    std::cout << std::flush;
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::compute() {
+    computeValue();
+    computeDerivatives();
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::determineClosestFrames() {
+    // Find the closest and the second closest frames
+    std::sort(frame_index.begin(), frame_index.end(), doCompareFrameDistance(*this));
+    // Determine the sign
+    sign = static_cast<long>(frame_index[0]) - static_cast<long>(frame_index[1]);
+    if (sign > 1) {
+        // sigma(z) is on the left side of the closest frame
+        sign = 1;
+    } else if (sign < -1) {
+        // sigma(z) is on the right side of the closest frame
+        sign = -1;
+    }
+    if (std::abs(static_cast<long>(frame_index[0]) - static_cast<long>(frame_index[1])) > 1) {
+        std::cout << "Warning: Geometrical pathCV relies on the assumption that the second closest frame is the neighbouring frame\n";
+        std::cout << "         Please check your configuration or increase restraint on z(σ)\n";
+        for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) {
+            std::cout << "Frame index: " << frame_index[i_frame] << " ; optimal RMSD = " << frame_distances[frame_index[i_frame]] << "\n";
+        }
+    }
+    min_frame_index_1 = frame_index[0];                                                         // s_m
+    min_frame_index_2 = use_second_closest_frame ? frame_index[1] : min_frame_index_1 - sign;   // s_(m-1)
+    min_frame_index_3 = use_third_closest_frame ? frame_index[2] : min_frame_index_1 + sign;    // s_(m+1)
+    m = static_cast<double>(frame_index[0]);
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::computeValue() {
+    updateReferenceDistances();
+    determineClosestFrames();
+    prepareVectors();
+    v1v1 = scalar_type();
+    v2v2 = scalar_type();
+    v3v3 = scalar_type();
+    v1v3 = scalar_type();
+    if (path_type == Z) {
+        v1v4 = scalar_type();
+        v4v4 = scalar_type();
+    }
+    for (size_t i_elem = 0; i_elem < v1.size(); ++i_elem) {
+        v1v1 += v1[i_elem] * v1[i_elem];
+        v2v2 += v2[i_elem] * v2[i_elem];
+        v3v3 += v3[i_elem] * v3[i_elem];
+        v1v3 += v1[i_elem] * v3[i_elem];
+        if (path_type == Z) {
+            v1v4 += v1[i_elem] * v4[i_elem];
+            v4v4 += v4[i_elem] * v4[i_elem];
+        }
+    }
+    f = (std::sqrt(v1v3 * v1v3 - v3v3 * (v1v1 - v2v2)) - v1v3) / v3v3;
+    if (path_type == Z) {
+        dx = 0.5 * (f - 1);
+        zz = v1v1 + 2 * dx * v1v4 + dx * dx * v4v4;
+        if (use_z_square) {
+            z = zz;
+        } else {
+            z = std::sqrt(std::fabs(zz));
+        }
+    }
+    if (path_type == S) {
+        s = m/M + static_cast<double>(sign) * ((f - 1) / (2 * M));
+    }
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::computeDerivatives() {
+    const scalar_type factor1 = 1.0 / (2.0 * v3v3 * std::sqrt(v1v3 * v1v3 - v3v3 * (v1v1 - v2v2)));
+    const scalar_type factor2 = 1.0 / v3v3;
+    for (size_t i_elem = 0; i_elem < v1.size(); ++i_elem) {
+        // Compute the derivative of f with vector v1
+        dfdv1[i_elem] = factor1 * (2.0 * v1v3 * v3[i_elem] - 2.0 * v3v3 * v1[i_elem]) - factor2 * v3[i_elem];
+        // Compute the derivative of f with respect to vector v2
+        dfdv2[i_elem] = factor1 * (2.0 * v3v3 * v2[i_elem]);
+        // dZ(v1(r), v2(r), v3) / dr = ∂Z/∂v1 * dv1/dr + ∂Z/∂v2 * dv2/dr
+        // dv1/dr = [fitting matrix 1][-1, ..., -1]
+        // dv2/dr = [fitting matrix 2][1, ..., 1]
+        // ∂Z/∂v1 = 1/(2*z) * (2v1 + (f-1)v4 + (v1⋅v4)∂f/∂v1 + v4^2 * 1/4 * 2(f-1) * ∂f/∂v1)
+        // ∂Z/∂v2 = 1/(2*z) * ((v1⋅v4)∂f/∂v2 + v4^2 * 1/4 * 2(f-1) * ∂f/∂v2)
+        if (path_type == Z) {
+            if (use_z_square) {
+                dzdv1[i_elem] = 2.0 * v1[i_elem] + (f-1) * v4[i_elem] + v1v4 * dfdv1[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv1[i_elem];
+                dzdv2[i_elem] = v1v4 * dfdv2[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv2[i_elem];
+            } else {
+                if (z > static_cast<scalar_type>(0)) {
+                    dzdv1[i_elem] = (1.0 / (2.0 * z)) * (2.0 * v1[i_elem] + (f-1) * v4[i_elem] + v1v4 * dfdv1[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv1[i_elem]);
+                    dzdv2[i_elem] = (1.0 / (2.0 * z)) * (v1v4 * dfdv2[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv2[i_elem]);
+                } else {
+                    // workaround at z = 0
+                    dzdv1[i_elem] = 0;
+                    dzdv2[i_elem] = 0;
+                }
+            }
+        }
+    }
+}
+
+}
+
+#endif // GEOMETRICPATHCV_H
diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp
index eeb7985fec..af17d8df66 100644
--- a/lib/colvars/colvaratoms.cpp
+++ b/lib/colvars/colvaratoms.cpp
@@ -178,6 +178,31 @@ int cvm::atom_group::remove_atom(cvm::atom_iter ai)
 }
 
 
+int cvm::atom_group::set_dummy()
+{
+  if (atoms_ids.size() > 0) {
+    return cvm::error("Error: setting group with keyword \""+key+
+                      "\" and name \""+name+"\" as dummy, but it already "
+                      "contains atoms.\n", INPUT_ERROR);
+  }
+  b_dummy = true;
+  return COLVARS_OK;
+}
+
+
+int cvm::atom_group::set_dummy_pos(cvm::atom_pos const &pos)
+{
+  if (b_dummy) {
+    dummy_atom_pos = pos;
+  } else {
+    return cvm::error("Error: setting dummy position for group with keyword \""+
+                      key+"\" and name \""+name+
+                      "\", but it is not dummy.\n", INPUT_ERROR);
+  }
+  return COLVARS_OK;
+}
+
+
 int cvm::atom_group::init()
 {
   if (!key.size()) key = "unnamed";
@@ -469,20 +494,15 @@ int cvm::atom_group::parse(std::string const &group_conf)
   // checks of doubly-counted atoms have been handled by add_atom() already
 
   if (get_keyval(group_conf, "dummyAtom", dummy_atom_pos, cvm::atom_pos())) {
-    b_dummy = true;
-    // note: atoms_ids.size() is used here in lieu of atoms.size(),
-    // which can be empty for scalable groups
-    if (atoms_ids.size()) {
-      cvm::error("Error: cannot set up group \""+
-                 key+"\" as a dummy atom "
-                 "and provide it with atom definitions.\n", INPUT_ERROR);
-    }
+
+    parse_error |= set_dummy();
+    parse_error |= set_dummy_pos(dummy_atom_pos);
+
   } else {
-    b_dummy = false;
 
     if (!(atoms_ids.size())) {
-      cvm::error("Error: no atoms defined for atom group \""+
-                 key+"\".\n", INPUT_ERROR);
+      parse_error |= cvm::error("Error: no atoms defined for atom group \""+
+                                key+"\".\n", INPUT_ERROR);
     }
 
     // whether these atoms will ever receive forces or not
diff --git a/lib/colvars/colvaratoms.h b/lib/colvars/colvaratoms.h
index 9756e0e364..c8b6ac4541 100644
--- a/lib/colvars/colvaratoms.h
+++ b/lib/colvars/colvaratoms.h
@@ -207,6 +207,12 @@ public:
   /// \brief Remove an atom object from this group
   int remove_atom(cvm::atom_iter ai);
 
+  /// Set this group as a dummy group (no actual atoms)
+  int set_dummy();
+
+  /// If this group is dummy, set the corresponding position
+  int set_dummy_pos(cvm::atom_pos const &pos);
+
   /// \brief Print the updated the total mass and charge of a group.
   /// This is needed in case the hosting MD code has an option to
   /// change atom masses after their initialization.
diff --git a/lib/colvars/colvarbias_meta.cpp b/lib/colvars/colvarbias_meta.cpp
index 27781ec733..8540e4a945 100644
--- a/lib/colvars/colvarbias_meta.cpp
+++ b/lib/colvars/colvarbias_meta.cpp
@@ -37,7 +37,6 @@ colvarbias_meta::colvarbias_meta(char const *key)
 {
   new_hills_begin = hills.end();
   hills_traj_os = NULL;
-  replica_hills_os = NULL;
 
   ebmeta_equil_steps = 0L;
 }
@@ -203,23 +202,37 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
     target_dist = new colvar_grid_scalar();
     target_dist->init_from_colvars(colvars);
     std::string target_dist_file;
-    get_keyval(conf, "targetdistfile", target_dist_file);
+    get_keyval(conf, "targetDistFile", target_dist_file);
     std::ifstream targetdiststream(target_dist_file.c_str());
     target_dist->read_multicol(targetdiststream);
     cvm::real min_val = target_dist->minimum_value();
+    cvm::real max_val = target_dist->maximum_value();
     if(min_val<0){
-      cvm::error("Error: Target distribution of ebMeta "
+      cvm::error("Error: Target distribution of EBMetaD "
                  "has negative values!.\n", INPUT_ERROR);
     }
-    cvm::real min_pos_val = target_dist->minimum_pos_value();
-    if(min_pos_val<=0){
-      cvm::error("Error: Target distribution of ebMeta has negative "
-                 "or zero minimum positive value!.\n", INPUT_ERROR);
-    }
-    if(min_val==0){
-      cvm::log("WARNING: Target distribution has zero values.\n");
-      cvm::log("Zeros will be converted to the minimum positive value.\n");
-      target_dist->remove_zeros(min_pos_val);
+    cvm::real target_dist_min_val;
+    get_keyval(conf, "targetDistMinVal", target_dist_min_val, 1/1000000.0);
+    if(target_dist_min_val>0 && target_dist_min_val<1){
+      target_dist_min_val=max_val*target_dist_min_val;
+      target_dist->remove_small_values(target_dist_min_val);
+    } else {
+      if (target_dist_min_val==0) {
+        cvm::log("NOTE: targetDistMinVal is set to zero, the minimum value of the target \n");
+        cvm::log(" distribution will be set as the minimum positive value.\n");
+        cvm::real min_pos_val = target_dist->minimum_pos_value();
+        if(min_pos_val<=0){
+          cvm::error("Error: Target distribution of EBMetaD has negative "
+                     "or zero minimum positive value!.\n", INPUT_ERROR);
+        }
+        if(min_val==0){
+          cvm::log("WARNING: Target distribution has zero values.\n");
+          cvm::log("Zeros will be converted to the minimum positive value.\n");
+          target_dist->remove_small_values(min_pos_val);
+        }
+      } else {
+          cvm::error("Error: targetDistMinVal must be a value between 0 and 1!.\n", INPUT_ERROR);
+      }
     }
     // normalize target distribution and multiply by effective volume = exp(differential entropy)
     target_dist->multiply_constant(1.0/target_dist->integral());
@@ -235,14 +248,14 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
 colvarbias_meta::~colvarbias_meta()
 {
   colvarbias_meta::clear_state_data();
+  colvarproxy *proxy = cvm::proxy;
 
-  if (replica_hills_os) {
-    cvm::proxy->close_output_stream(replica_hills_file);
-    replica_hills_os = NULL;
+  if (proxy->get_output_stream(replica_hills_file)) {
+    proxy->close_output_stream(replica_hills_file);
   }
 
   if (hills_traj_os) {
-    cvm::proxy->close_output_stream(hills_traj_file_name());
+    proxy->close_output_stream(hills_traj_file_name());
     hills_traj_os = NULL;
   }
 
@@ -523,6 +536,8 @@ int colvarbias_meta::update_bias()
 
     case multiple_replicas:
       create_hill(hill(hill_weight*hills_scale, colvars, hill_width, replica_id));
+      std::ostream *replica_hills_os =
+        cvm::proxy->get_output_stream(replica_hills_file);
       if (replica_hills_os) {
         *replica_hills_os << hills.back();
       } else {
@@ -921,13 +936,16 @@ void colvarbias_meta::recount_hills_off_grid(colvarbias_meta::hill_iter  h_first
 
 int colvarbias_meta::replica_share()
 {
+  colvarproxy *proxy = cvm::proxy;
   // sync with the other replicas (if needed)
   if (comm == multiple_replicas) {
     // reread the replicas registry
     update_replicas_registry();
     // empty the output buffer
+    std::ostream *replica_hills_os =
+      proxy->get_output_stream(replica_hills_file);
     if (replica_hills_os) {
-      cvm::proxy->flush_output_stream(replica_hills_os);
+      proxy->flush_output_stream(replica_hills_os);
     }
     read_replica_files();
   }
@@ -1089,11 +1107,7 @@ void colvarbias_meta::read_replica_files()
                (replicas[ir])->replica_state_file+"\".\n");
 
       std::ifstream is((replicas[ir])->replica_state_file.c_str());
-      if (! (replicas[ir])->read_state(is)) {
-        cvm::log("Reading from file \""+(replicas[ir])->replica_state_file+
-                 "\" failed or incomplete: will try again in "+
-                 cvm::to_str(replica_update_freq)+" steps.\n");
-      } else {
+      if ((replicas[ir])->read_state(is)) {
         // state file has been read successfully
         (replicas[ir])->replica_state_file_in_sync = true;
         (replicas[ir])->update_status = 0;
@@ -1550,15 +1564,11 @@ int colvarbias_meta::setup_output()
     // for the others to read
 
     // open the "hills" buffer file
-    if (!replica_hills_os) {
-      cvm::proxy->backup_file(replica_hills_file);
-      replica_hills_os = cvm::proxy->output_stream(replica_hills_file);
-      if (!replica_hills_os) return cvm::get_error();
-      replica_hills_os->setf(std::ios::scientific, std::ios::floatfield);
-    }
+    reopen_replica_buffer_file();
 
     // write the state file (so that there is always one available)
     write_replica_state_file();
+
     // schedule to read the state files of the other replicas
     for (size_t ir = 0; ir < replicas.size(); ir++) {
       (replicas[ir])->replica_state_file_in_sync = false;
@@ -1661,15 +1671,16 @@ std::ostream & colvarbias_meta::write_state_data(std::ostream& os)
 
 int colvarbias_meta::write_state_to_replicas()
 {
+  int error_code = COLVARS_OK;
   if (comm != single_replica) {
-    write_replica_state_file();
-    // schedule to reread the state files of the other replicas (they
-    // have also rewritten them)
+    error_code |= write_replica_state_file();
+    error_code |= reopen_replica_buffer_file();
+    // schedule to reread the state files of the other replicas
     for (size_t ir = 0; ir < replicas.size(); ir++) {
       (replicas[ir])->replica_state_file_in_sync = false;
     }
   }
-  return COLVARS_OK;
+  return error_code;
 }
 
 
@@ -1693,6 +1704,20 @@ void colvarbias_meta::write_pmf()
     // output the PMF from this instance or replica
     pmf->reset();
     pmf->add_grid(*hills_energy);
+
+    if (ebmeta) {
+      int nt_points=pmf->number_of_points();
+      for (int i = 0; i < nt_points; i++) {
+         cvm:: real pmf_val=0.0;
+         cvm:: real target_val=target_dist->value(i);
+         if (target_val>0) {
+           pmf_val=pmf->value(i);
+           pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * std::log(target_val);
+         }
+         pmf->set_value(i,pmf_val);
+      }
+    }
+
     cvm::real const max = pmf->maximum_value();
     pmf->add_constant(-1.0 * max);
     pmf->multiply_constant(-1.0);
@@ -1716,10 +1741,24 @@ void colvarbias_meta::write_pmf()
   if (comm != single_replica) {
     // output the combined PMF from all replicas
     pmf->reset();
-    pmf->add_grid(*hills_energy);
+    // current replica already included in the pools of replicas
     for (size_t ir = 0; ir < replicas.size(); ir++) {
       pmf->add_grid(*(replicas[ir]->hills_energy));
     }
+
+    if (ebmeta) {
+      int nt_points=pmf->number_of_points();
+      for (int i = 0; i < nt_points; i++) {
+         cvm:: real pmf_val=0.0;
+         cvm:: real target_val=target_dist->value(i);
+         if (target_val>0) {
+           pmf_val=pmf->value(i);
+           pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * std::log(target_val);
+         }
+         pmf->set_value(i,pmf_val);
+      }
+    }
+
     cvm::real const max = pmf->maximum_value();
     pmf->add_constant(-1.0 * max);
     pmf->multiply_constant(-1.0);
@@ -1744,74 +1783,47 @@ void colvarbias_meta::write_pmf()
 
 int colvarbias_meta::write_replica_state_file()
 {
+  colvarproxy *proxy = cvm::proxy;
+
   if (cvm::debug()) {
     cvm::log("Writing replica state file for bias \""+name+"\"\n");
   }
-  // write down also the restart for the other replicas
-  cvm::backup_file(replica_state_file.c_str());
-  std::ostream *rep_state_os = cvm::proxy->output_stream(replica_state_file);
-  if (rep_state_os == NULL) {
-    cvm::error("Error: in opening file \""+
-               replica_state_file+"\" for writing.\n", FILE_ERROR);
-    return FILE_ERROR;
+
+  int error_code = COLVARS_OK;
+
+  // Write to temporary state file
+  std::string const tmp_state_file(replica_state_file+".tmp");
+  error_code |= proxy->remove_file(tmp_state_file);
+  std::ostream *rep_state_os = cvm::proxy->output_stream(tmp_state_file);
+  if (rep_state_os) {
+    if (!write_state(*rep_state_os)) {
+      error_code |= cvm::error("Error: in writing to temporary file \""+
+                               tmp_state_file+"\".\n", FILE_ERROR);
+    }
   }
+  error_code |= proxy->close_output_stream(tmp_state_file);
 
-  rep_state_os->setf(std::ios::scientific, std::ios::floatfield);
+  error_code |= proxy->rename_file(tmp_state_file, replica_state_file);
 
-  if (!write_state(*rep_state_os)) {
-    cvm::error("Error: in writing to file \""+
-               replica_state_file+"\".\n", FILE_ERROR);
-    cvm::proxy->close_output_stream(replica_state_file);
-    return FILE_ERROR;
+  return error_code;
+}
+
+
+int colvarbias_meta::reopen_replica_buffer_file()
+{
+  int error_code = COLVARS_OK;
+  colvarproxy *proxy = cvm::proxy;
+  if (proxy->get_output_stream(replica_hills_file) != NULL) {
+    error_code |= proxy->close_output_stream(replica_hills_file);
   }
-
-  cvm::proxy->close_output_stream(replica_state_file);
-
-  // rep_state_os.setf(std::ios::scientific, std::ios::floatfield);
-  // rep_state_os << "\n"
-  //              << "metadynamics {\n"
-  //              << "  configuration {\n"
-  //              << "    name " << this->name << "\n"
-  //              << "    step " << cvm::step_absolute() << "\n";
-  // if (this->comm != single_replica) {
-  //   rep_state_os << "    replicaID " << this->replica_id << "\n";
-  // }
-  // rep_state_os << "  }\n\n";
-  // rep_state_os << "  hills_energy\n";
-  // rep_state_os << std::setprecision(cvm::cv_prec)
-  //              << std::setw(cvm::cv_width);
-  // hills_energy->write_restart(rep_state_os);
-  // rep_state_os << "  hills_energy_gradients\n";
-  // rep_state_os << std::setprecision(cvm::cv_prec)
-  //              << std::setw(cvm::cv_width);
-  // hills_energy_gradients->write_restart(rep_state_os);
-
-  // if ( (!use_grids) || keep_hills ) {
-  //   // write all hills currently in memory
-  //   for (std::list<hill>::const_iterator h = this->hills.begin();
-  //        h != this->hills.end();
-  //        h++) {
-  //     rep_state_os << *h;
-  //   }
-  // } else {
-  //   // write just those that are near the grid boundaries
-  //   for (std::list<hill>::const_iterator h = this->hills_off_grid.begin();
-  //        h != this->hills_off_grid.end();
-  //        h++) {
-  //     rep_state_os << *h;
-  //   }
-  // }
-  // rep_state_os << "}\n\n";
-  // rep_state_os.close();
-
-  // reopen the hills file
-  cvm::proxy->close_output_stream(replica_hills_file);
-  cvm::proxy->backup_file(replica_hills_file);
-  replica_hills_os = cvm::proxy->output_stream(replica_hills_file);
-  if (!replica_hills_os) return cvm::get_error();
-  replica_hills_os->setf(std::ios::scientific, std::ios::floatfield);
-
-  return COLVARS_OK;
+  error_code |= proxy->remove_file(replica_hills_file);
+  std::ostream *replica_hills_os = proxy->output_stream(replica_hills_file);
+  if (replica_hills_os) {
+    replica_hills_os->setf(std::ios::scientific, std::ios::floatfield);
+  } else {
+    error_code |= FILE_ERROR;
+  }
+  return error_code;
 }
 
 
@@ -1883,5 +1895,3 @@ std::ostream & operator << (std::ostream &os, colvarbias_meta::hill const &h)
 
   return os;
 }
-
-
diff --git a/lib/colvars/colvarbias_meta.h b/lib/colvars/colvarbias_meta.h
index 0ba2bef1c3..8e98274b2d 100644
--- a/lib/colvars/colvarbias_meta.h
+++ b/lib/colvars/colvarbias_meta.h
@@ -215,9 +215,12 @@ protected:
   /// \brief Read new data from replicas' files
   virtual void read_replica_files();
 
-  /// \brief Write data to other replicas
+  /// Write full state information to be read by other replicas
   virtual int write_replica_state_file();
 
+  /// Call this after write_replica_state_file()
+  virtual int reopen_replica_buffer_file();
+
   /// \brief Additional, "mirror" metadynamics biases, to collect info
   /// from the other replicas
   ///
@@ -251,9 +254,6 @@ protected:
   /// This file becomes empty after replica_state_file is rewritten
   std::string            replica_hills_file;
 
-  /// \brief Output stream corresponding to replica_hills_file
-  std::ostream          *replica_hills_os;
-
   /// Position within replica_hills_file (when reading it)
   int                    replica_hills_file_pos;
 
diff --git a/lib/colvars/colvarbias_restraint.cpp b/lib/colvars/colvarbias_restraint.cpp
index 90588f5a1f..ab02820cf0 100644
--- a/lib/colvars/colvarbias_restraint.cpp
+++ b/lib/colvars/colvarbias_restraint.cpp
@@ -1295,7 +1295,8 @@ colvarvalue const colvarbias_restraint_linear::restraint_force(size_t i) const
 
 cvm::real colvarbias_restraint_linear::d_restraint_potential_dk(size_t i) const
 {
-  return 1.0 / variables(i)->width * (variables(i)->value() - colvar_centers[i]);
+  return 1.0 / variables(i)->width * (variables(i)->value() -
+                                      colvar_centers[i]).sum();
 }
 
 
diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp
index 3075ed82ca..431884a877 100644
--- a/lib/colvars/colvarcomp.cpp
+++ b/lib/colvars/colvarcomp.cpp
@@ -7,6 +7,8 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
+#include <algorithm>
+
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvar.h"
diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h
index f615680ba6..1d95cbe600 100644
--- a/lib/colvars/colvarcomp.h
+++ b/lib/colvars/colvarcomp.h
@@ -24,6 +24,13 @@
 #include "colvar.h"
 #include "colvaratoms.h"
 
+#if (__cplusplus >= 201103L)
+#include "colvar_geometricpath.h"
+#include <functional>
+#endif // C++11 checking
+
+#include <map>
+
 
 /// \brief Colvar component (base class for collective variables)
 ///
@@ -688,9 +695,6 @@ protected:
   /// Reference coordinates
   std::vector<cvm::atom_pos>  ref_pos;
 
-  /// Geometric center of the reference coordinates
-  cvm::atom_pos                ref_pos_center;
-
   /// Eigenvector (of a normal or essential mode): will always have zero center
   std::vector<cvm::rvector>   eigenvec;
 
@@ -883,9 +887,8 @@ protected:
   /// Integer exponent of the function denominator
   int ed;
 
-  /// \brief If true, group2 will be treated as a single atom, stored in this
-  /// accessory group
-  cvm::atom_group *group2_center;
+  /// If true, group2 will be treated as a single atom
+  bool b_group2_center_only;
 
   /// Tolerance for the pair list
   cvm::real tolerance;
@@ -937,9 +940,12 @@ public:
                                       bool **pairlist_elem,
                                       cvm::real tolerance);
 
-  /// Main workhorse function
+  /// Workhorse function
   template<int flags> int compute_coordnum();
 
+  /// Workhorse function
+  template<int flags> void main_loop(bool **pairlist_elem);
+
 };
 
 
@@ -1383,6 +1389,222 @@ public:
 };
 
 
+
+class colvar::componentDisabled
+  : public colvar::cvc
+{
+public:
+    componentDisabled(std::string const &conf) {
+        cvm::error("Error: this component is not enabled in the current build; please see https://colvars.github.io/README-c++11.html");
+    }
+    virtual ~componentDisabled() {}
+    virtual void calc_value() {}
+    virtual void calc_gradients() {}
+    virtual void apply_force(colvarvalue const &force) {}
+};
+
+
+
+#if (__cplusplus >= 201103L)
+class colvar::CartesianBasedPath
+  : public colvar::cvc
+{
+protected:
+    virtual void computeReferenceDistance(std::vector<cvm::real>& result);
+    /// Selected atoms
+    cvm::atom_group *atoms;
+    /// Fitting options
+    bool has_user_defined_fitting;
+    /// Reference frames
+    std::vector<std::vector<cvm::atom_pos>> reference_frames;
+    std::vector<std::vector<cvm::atom_pos>> reference_fitting_frames;
+    /// Atom groups for RMSD calculation together with reference frames
+    std::vector<cvm::atom_group*> comp_atoms;
+    /// Total number of reference frames
+    size_t total_reference_frames;
+public:
+    CartesianBasedPath(std::string const &conf);
+    virtual ~CartesianBasedPath();
+    virtual void calc_value() = 0;
+    virtual void apply_force(colvarvalue const &force) = 0;
+};
+
+/// \brief Colvar component: alternative path collective variable using geometry, variable s
+/// For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html
+/// Díaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601.
+class colvar::gspath
+  : public colvar::CartesianBasedPath, public GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::S>
+{
+private:
+    // Optimal rotation for compute v3
+    cvm::rotation rot_v3;
+protected:
+    virtual void prepareVectors();
+    virtual void updateReferenceDistances();
+public:
+    gspath(std::string const &conf);
+    virtual ~gspath() {}
+    virtual void calc_value();
+    virtual void calc_gradients();
+    virtual void apply_force(colvarvalue const &force);
+};
+
+
+
+/// \brief Colvar component: alternative path collective variable using geometry, variable z
+/// This should be merged with gspath in the same class by class inheritance or something else
+class colvar::gzpath
+  : public colvar::CartesianBasedPath, public GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::Z>
+{
+private:
+    // Optimal rotation for compute v3, v4
+    cvm::rotation rot_v3;
+    cvm::rotation rot_v4;
+protected:
+    virtual void prepareVectors();
+    virtual void updateReferenceDistances();
+public:
+    gzpath(std::string const &conf);
+    virtual ~gzpath() {}
+    virtual void calc_value();
+    virtual void calc_gradients();
+    virtual void apply_force(colvarvalue const &force);
+};
+
+/// Current only linear combination of sub-CVCs is available
+class colvar::linearCombination
+  : public colvar::cvc
+{
+protected:
+    /// Map from string to the types of colvar components
+    std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> string_cv_map;
+    /// Sub-colvar components
+    std::vector<colvar::cvc*> cv;
+    /// If all sub-cvs use explicit gradients then we also use it
+    bool use_explicit_gradients;
+protected:
+    cvm::real getPolynomialFactorOfCVGradient(size_t i_cv) const;
+public:
+    linearCombination(std::string const &conf);
+    virtual ~linearCombination();
+    virtual void calc_value();
+    virtual void calc_gradients();
+    virtual void apply_force(colvarvalue const &force);
+};
+
+
+class colvar::CVBasedPath
+  : public colvar::cvc
+{
+protected:
+    /// Map from string to the types of colvar components
+    std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> string_cv_map;
+    /// Sub-colvar components
+    std::vector<colvar::cvc*> cv;
+    /// Refernce colvar values from path
+    std::vector<std::vector<colvarvalue>> ref_cv;
+    /// If all sub-cvs use explicit gradients then we also use it
+    bool use_explicit_gradients;
+    /// Total number of reference frames
+    size_t total_reference_frames;
+protected:
+    virtual void computeReferenceDistance(std::vector<cvm::real>& result);
+    cvm::real getPolynomialFactorOfCVGradient(size_t i_cv) const;
+public:
+    CVBasedPath(std::string const &conf);
+    virtual ~CVBasedPath();
+    virtual void calc_value() = 0;
+    virtual void apply_force(colvarvalue const &force) = 0;
+};
+
+
+/// \brief Colvar component: alternative path collective variable using geometry, variable s
+/// Allow any combination of existing (scalar) CVs
+/// For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html
+/// Díaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601.
+class colvar::gspathCV
+  : public colvar::CVBasedPath, public GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::S>
+{
+protected:
+    virtual void updateReferenceDistances();
+    virtual void prepareVectors();
+public:
+    gspathCV(std::string const &conf);
+    virtual ~gspathCV();
+    virtual void calc_value();
+    virtual void calc_gradients();
+    virtual void apply_force(colvarvalue const &force);
+};
+
+
+
+class colvar::gzpathCV
+  : public colvar::CVBasedPath, public GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::Z>
+{
+protected:
+    virtual void updateReferenceDistances();
+    virtual void prepareVectors();
+public:
+    gzpathCV(std::string const &conf);
+    virtual ~gzpathCV();
+    virtual void calc_value();
+    virtual void calc_gradients();
+    virtual void apply_force(colvarvalue const &force);
+};
+
+#else // if the compiler doesn't support C++11
+
+class colvar::linearCombination
+  : public colvar::componentDisabled
+{
+public:
+    linearCombination(std::string const &conf) : componentDisabled(conf) {}
+};
+
+class colvar::CartesianBasedPath
+  : public colvar::componentDisabled
+{
+public:
+    CartesianBasedPath(std::string const &conf) : componentDisabled(conf) {}
+};
+
+class colvar::CVBasedPath
+  : public colvar::componentDisabled
+{
+public:
+    CVBasedPath(std::string const &conf) : componentDisabled(conf) {}
+};
+
+class colvar::gspath
+  : public colvar::componentDisabled
+{
+public:
+    gspath(std::string const &conf) : componentDisabled(conf) {}
+};
+
+class colvar::gzpath
+  : public colvar::componentDisabled
+{
+public:
+    gzpath(std::string const &conf) : componentDisabled(conf) {}
+};
+
+class colvar::gspathCV
+  : public colvar::componentDisabled
+{
+public:
+    gspathCV(std::string const &conf) : componentDisabled(conf) {}
+};
+
+class colvar::gzpathCV
+  : public colvar::componentDisabled
+{
+public:
+    gzpathCV(std::string const &conf) : componentDisabled(conf) {}
+};
+
+#endif // C++11 checking
+
 // metrics functions for cvc implementations
 
 // simple definitions of the distance functions; these are useful only
diff --git a/lib/colvars/colvarcomp_coordnums.cpp b/lib/colvars/colvarcomp_coordnums.cpp
index 059b0c825b..b6dd6535ef 100644
--- a/lib/colvars/colvarcomp_coordnums.cpp
+++ b/lib/colvars/colvarcomp_coordnums.cpp
@@ -91,7 +91,7 @@ cvm::real colvar::coordnum::switching_function(cvm::real const &r0,
 
 
 colvar::coordnum::coordnum(std::string const &conf)
-  : cvc(conf), b_anisotropic(false), group2_center(NULL), pairlist(NULL)
+  : cvc(conf), b_anisotropic(false), pairlist(NULL)
 
 {
   function_type = "coordnum";
@@ -156,14 +156,7 @@ colvar::coordnum::coordnum(std::string const &conf)
     cvm::log("Warning: only minimum-image distances are used by this variable.\n");
   }
 
-  bool b_group2_center_only = false;
   get_keyval(conf, "group2CenterOnly", b_group2_center_only, group2->b_dummy);
-  if (b_group2_center_only) {
-    if (!group2_center) {
-      group2_center = new cvm::atom_group();
-      group2_center->add_atom(cvm::atom());
-    }
-  }
 
   get_keyval(conf, "tolerance", tolerance, 0.0);
   if (tolerance > 0) {
@@ -185,7 +178,7 @@ colvar::coordnum::coordnum(std::string const &conf)
 
 
 colvar::coordnum::coordnum()
-  : b_anisotropic(false), group2_center(NULL), pairlist(NULL)
+  : b_anisotropic(false), pairlist(NULL)
 {
   function_type = "coordnum";
   x.type(colvarvalue::type_scalar);
@@ -197,69 +190,60 @@ colvar::coordnum::~coordnum()
   if (pairlist != NULL) {
     delete [] pairlist;
   }
-  if (group2_center != NULL) {
-    delete group2_center;
+}
+
+
+template<int flags> void colvar::coordnum::main_loop(bool **pairlist_elem)
+{
+  if (b_group2_center_only) {
+    cvm::atom group2_com_atom;
+    group2_com_atom.pos = group2->center_of_mass();
+    for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++) {
+      x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
+                                                *ai1, group2_com_atom,
+                                                pairlist_elem,
+                                                tolerance);
+    }
+    if (b_group2_center_only) {
+      group2->set_weighted_gradient(group2_com_atom.grad);
+    }
+  } else {
+    for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++) {
+      for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
+        x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
+                                                  *ai1, *ai2,
+                                                  pairlist_elem,
+                                                  tolerance);
+      }
+    }
   }
 }
 
 
 template<int compute_flags> int colvar::coordnum::compute_coordnum()
 {
-  if (group2_center) {
-    (*group2_center)[0].pos = group2->center_of_mass();
-    group2_center->calc_required_properties();
-  }
-  cvm::atom_group *group2p = group2_center ? group2_center : group2;
-
   bool const use_pairlist = (pairlist != NULL);
   bool const rebuild_pairlist = (pairlist != NULL) &&
     (cvm::step_relative() % pairlist_freq == 0);
 
   bool *pairlist_elem = use_pairlist ? pairlist : NULL;
-  cvm::atom_iter ai1 = group1->begin(), ai2 = group2p->begin();
-  cvm::atom_iter const ai1_end = group1->end();
-  cvm::atom_iter const ai2_end = group2p->end();
 
   if (b_anisotropic) {
 
     if (use_pairlist) {
-
       if (rebuild_pairlist) {
-
         int const flags = compute_flags | ef_anisotropic | ef_use_pairlist |
           ef_rebuild_pairlist;
-        for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
-          for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
-            x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
-                                                      *ai1, *ai2,
-                                                      &pairlist_elem,
-                                                      tolerance);
-          }
-        }
-
+        main_loop<flags>(&pairlist_elem);
       } else {
-
         int const flags = compute_flags | ef_anisotropic | ef_use_pairlist;
-        for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
-          for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
-            x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
-                                                      *ai1, *ai2,
-                                                      &pairlist_elem,
-                                                      tolerance);
-          }
-        }
+        main_loop<flags>(&pairlist_elem);
       }
 
-    } else { // if (use_pairlist) {
+    } else {
 
       int const flags = compute_flags | ef_anisotropic;
-      for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
-        for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
-          x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
-                                                    *ai1, *ai2,
-                                                    NULL, 0.0);
-        }
-      }
+      main_loop<flags>(NULL);
     }
 
   } else {
@@ -267,46 +251,17 @@ template<int compute_flags> int colvar::coordnum::compute_coordnum()
     if (use_pairlist) {
 
       if (rebuild_pairlist) {
-
         int const flags = compute_flags | ef_use_pairlist | ef_rebuild_pairlist;
-        for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
-          for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
-            x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
-                                                      *ai1, *ai2,
-                                                      &pairlist_elem,
-                                                      tolerance);
-          }
-        }
-
+        main_loop<flags>(&pairlist_elem);
       } else {
-
         int const flags = compute_flags | ef_use_pairlist;
-        for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
-          for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
-            x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
-                                                      *ai1, *ai2,
-                                                      &pairlist_elem,
-                                                      tolerance);
-          }
-        }
+        main_loop<flags>(&pairlist_elem);
       }
 
-    } else { // if (use_pairlist) {
+    } else {
 
       int const flags = compute_flags;
-      for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
-        for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
-          x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
-                                                    *ai1, *ai2,
-                                                    NULL, 0.0);
-        }
-      }
-    }
-  }
-
-  if (compute_flags & ef_gradients) {
-    if (group2_center) {
-      group2->set_weighted_gradient((*group2_center)[0].grad);
+      main_loop<flags>(NULL);
     }
   }
 
diff --git a/lib/colvars/colvarcomp_distances.cpp b/lib/colvars/colvarcomp_distances.cpp
index d9cd9d55e4..7cb4c30c31 100644
--- a/lib/colvars/colvarcomp_distances.cpp
+++ b/lib/colvars/colvarcomp_distances.cpp
@@ -1013,8 +1013,7 @@ colvar::rmsd::rmsd(std::string const &conf)
                   cvm::to_str(atoms->size())+").\n");
       return;
     }
-  }
-  {
+  } else { // Only look for ref pos file if ref positions not already provided
     std::string ref_pos_file;
     if (get_keyval(conf, "refPositionsFile", ref_pos_file, std::string(""))) {
 
@@ -1041,12 +1040,15 @@ colvar::rmsd::rmsd(std::string const &conf)
 
       cvm::load_coords(ref_pos_file.c_str(), &ref_pos, atoms,
                        ref_pos_col, ref_pos_col_value);
+    } else {
+      cvm::error("Error: no reference positions for RMSD; use either refPositions of refPositionsFile.");
+      return;
     }
   }
 
   if (ref_pos.size() != atoms->size()) {
     cvm::error("Error: found " + cvm::to_str(ref_pos.size()) +
-                    " reference positions; expected " + cvm::to_str(atoms->size()));
+                    " reference positions for RMSD; expected " + cvm::to_str(atoms->size()));
     return;
   }
 
diff --git a/lib/colvars/colvarcomp_gpath.cpp b/lib/colvars/colvarcomp_gpath.cpp
new file mode 100644
index 0000000000..530aaf3284
--- /dev/null
+++ b/lib/colvars/colvarcomp_gpath.cpp
@@ -0,0 +1,910 @@
+#if (__cplusplus >= 201103L)
+
+// This file is part of the Collective Variables module (Colvars).
+// The original version of Colvars and its updates are located at:
+// https://github.com/colvars/colvars
+// Please update all Colvars source files before making any changes.
+// If you wish to distribute your changes, please submit them to the
+// Colvars repository at GitHub.
+
+#include <numeric>
+#include <algorithm>
+#include <cmath>
+#include <cstdlib>
+#include <limits>
+
+#include "colvarmodule.h"
+#include "colvarvalue.h"
+#include "colvarparse.h"
+#include "colvar.h"
+#include "colvarcomp.h"
+
+namespace GeometricPathCV {
+void init_string_cv_map(std::map<std::string, std::function<colvar::cvc* (const std::string& conf)>>& string_cv_map);
+}
+
+bool compareColvarComponent(colvar::cvc *i, colvar::cvc *j)
+{
+    return i->name < j->name;
+}
+
+colvar::CartesianBasedPath::CartesianBasedPath(std::string const &conf): cvc(conf), atoms(nullptr), reference_frames(0) {
+    // Parse selected atoms
+    atoms = parse_group(conf, "atoms");
+    has_user_defined_fitting = false;
+    std::string fitting_conf;
+    if (key_lookup(conf, "fittingAtoms", &fitting_conf)) {
+        has_user_defined_fitting = true;
+    }
+    // Lookup reference column of PDB
+    // Copied from the RMSD class
+    std::string reference_column;
+    double reference_column_value;
+    if (get_keyval(conf, "refPositionsCol", reference_column, std::string(""))) {
+        bool found = get_keyval(conf, "refPositionsColValue", reference_column_value, 0.0);
+        if (found && reference_column_value == 0.0) {
+          cvm::error("Error: refPositionsColValue, "
+                     "if provided, must be non-zero.\n");
+          return;
+        }
+    }
+    // Lookup all reference frames
+    bool has_frames = true;
+    total_reference_frames = 0;
+    while (has_frames) {
+        std::string reference_position_file_lookup = "refPositionsFile" + cvm::to_str(total_reference_frames + 1);
+        if (key_lookup(conf, reference_position_file_lookup.c_str())) {
+            std::string reference_position_filename;
+            get_keyval(conf, reference_position_file_lookup.c_str(), reference_position_filename, std::string(""));
+            std::vector<cvm::atom_pos> reference_position(atoms->size());
+            cvm::load_coords(reference_position_filename.c_str(), &reference_position, atoms, reference_column, reference_column_value);
+            reference_frames.push_back(reference_position);
+            ++total_reference_frames;
+        } else {
+            has_frames = false;
+        }
+    }
+    // Setup alignment to compute RMSD with respect to reference frames
+    for (size_t i_frame = 0; i_frame < reference_frames.size(); ++i_frame) {
+        cvm::atom_group* tmp_atoms = parse_group(conf, "atoms");
+        if (!has_user_defined_fitting) {
+            // Swipe from the rmsd class
+            tmp_atoms->b_center = true;
+            tmp_atoms->b_rotate = true;
+            tmp_atoms->ref_pos = reference_frames[i_frame];
+            tmp_atoms->center_ref_pos();
+            tmp_atoms->enable(f_ag_fit_gradients);
+            tmp_atoms->rot.request_group1_gradients(tmp_atoms->size());
+            tmp_atoms->rot.request_group2_gradients(tmp_atoms->size());
+            comp_atoms.push_back(tmp_atoms);
+        } else {
+            // parse a group of atoms for fitting
+            std::string fitting_group_name = std::string("fittingAtoms") + cvm::to_str(i_frame);
+            cvm::atom_group* tmp_fitting_atoms = new cvm::atom_group(fitting_group_name.c_str());
+            tmp_fitting_atoms->parse(fitting_conf);
+            tmp_fitting_atoms->disable(f_ag_scalable);
+            tmp_fitting_atoms->disable(f_ag_scalable_com);
+            tmp_fitting_atoms->fit_gradients.assign(tmp_fitting_atoms->size(), cvm::atom_pos(0.0, 0.0, 0.0));
+            std::string reference_position_file_lookup = "refPositionsFile" + cvm::to_str(i_frame + 1);
+            std::string reference_position_filename;
+            get_keyval(conf, reference_position_file_lookup.c_str(), reference_position_filename, std::string(""));
+            std::vector<cvm::atom_pos> reference_fitting_position(tmp_fitting_atoms->size());
+            cvm::load_coords(reference_position_filename.c_str(), &reference_fitting_position, tmp_fitting_atoms, reference_column, reference_column_value);
+            // setup the atom group for calculating
+            tmp_atoms->b_center = true;
+            tmp_atoms->b_rotate = true;
+            tmp_atoms->b_user_defined_fit = true;
+            tmp_atoms->disable(f_ag_scalable);
+            tmp_atoms->disable(f_ag_scalable_com);
+            tmp_atoms->ref_pos = reference_fitting_position;
+            tmp_atoms->center_ref_pos();
+            tmp_atoms->enable(f_ag_fit_gradients);
+            tmp_atoms->enable(f_ag_fitting_group);
+            tmp_atoms->fitting_group = tmp_fitting_atoms;
+            tmp_atoms->rot.request_group1_gradients(tmp_fitting_atoms->size());
+            tmp_atoms->rot.request_group2_gradients(tmp_fitting_atoms->size());
+            reference_fitting_frames.push_back(reference_fitting_position);
+            comp_atoms.push_back(tmp_atoms);
+        }
+    }
+    x.type(colvarvalue::type_scalar);
+    // Don't use implicit gradient
+    enable(f_cvc_explicit_gradient);
+}
+
+colvar::CartesianBasedPath::~CartesianBasedPath() {
+    for (auto it_comp_atoms = comp_atoms.begin(); it_comp_atoms != comp_atoms.end(); ++it_comp_atoms) {
+        if (*it_comp_atoms != nullptr) {
+            delete (*it_comp_atoms);
+            (*it_comp_atoms) = nullptr;
+        }
+    }
+}
+
+void colvar::CartesianBasedPath::computeReferenceDistance(std::vector<cvm::real>& result) {
+    for (size_t i_frame = 0; i_frame < reference_frames.size(); ++i_frame) {
+        cvm::real frame_rmsd = 0.0;
+        for (size_t i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            frame_rmsd += ((*(comp_atoms[i_frame]))[i_atom].pos - reference_frames[i_frame][i_atom]).norm2();
+        }
+        frame_rmsd /= cvm::real(atoms->size());
+        frame_rmsd = cvm::sqrt(frame_rmsd);
+        result[i_frame] = frame_rmsd;
+    }
+}
+
+colvar::gspath::gspath(std::string const &conf): CartesianBasedPath(conf) {
+    function_type = "gspath";
+    get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
+    if (use_second_closest_frame == true) {
+        cvm::log(std::string("Geometric path s(σ) will use the second closest frame to compute s_(m-1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m-1)\n"));
+    }
+    get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false);
+    if (use_third_closest_frame == true) {
+        cvm::log(std::string("Geometric path s(σ) will use the third closest frame to compute s_(m+1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m+1)\n"));
+    }
+    GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::S>::initialize(atoms->size(), cvm::atom_pos(), total_reference_frames, use_second_closest_frame, use_third_closest_frame);
+    cvm::log(std::string("Geometric pathCV(s) is initialized.\n"));
+    cvm::log(std::string("Geometric pathCV(s) loaded ") + cvm::to_str(reference_frames.size()) + std::string(" frames.\n"));
+}
+
+void colvar::gspath::updateReferenceDistances() {
+    computeReferenceDistance(frame_distances);
+}
+
+void colvar::gspath::prepareVectors() {
+    size_t i_atom;
+    for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+        // v1 = s_m - z
+        v1[i_atom] = reference_frames[min_frame_index_1][i_atom] - (*(comp_atoms[min_frame_index_1]))[i_atom].pos;
+        // v2 = z - s_(m-1)
+        v2[i_atom] = (*(comp_atoms[min_frame_index_2]))[i_atom].pos - reference_frames[min_frame_index_2][i_atom];
+    }
+    if (min_frame_index_3 < 0 || min_frame_index_3 > M) {
+        cvm::atom_pos reference_cog_1, reference_cog_2;
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            reference_cog_1 += reference_frames[min_frame_index_1][i_atom];
+            reference_cog_2 += reference_frames[min_frame_index_2][i_atom];
+        }
+        reference_cog_1 /= reference_frames[min_frame_index_1].size();
+        reference_cog_2 /= reference_frames[min_frame_index_2].size();
+        std::vector<cvm::atom_pos> tmp_reference_frame_1(reference_frames[min_frame_index_1].size());
+        std::vector<cvm::atom_pos> tmp_reference_frame_2(reference_frames[min_frame_index_2].size());
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            tmp_reference_frame_1[i_atom] = reference_frames[min_frame_index_1][i_atom] - reference_cog_1;
+            tmp_reference_frame_2[i_atom] = reference_frames[min_frame_index_2][i_atom] - reference_cog_2;
+        }
+        if (has_user_defined_fitting) {
+            cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_2;
+            for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
+                reference_fitting_cog_1 += reference_fitting_frames[min_frame_index_1][i_atom];
+                reference_fitting_cog_2 += reference_fitting_frames[min_frame_index_2][i_atom];
+            }
+            reference_fitting_cog_1 /= reference_fitting_frames[min_frame_index_1].size();
+            reference_fitting_cog_2 /= reference_fitting_frames[min_frame_index_2].size();
+            std::vector<cvm::atom_pos> tmp_reference_fitting_frame_1(reference_fitting_frames[min_frame_index_1].size());
+            std::vector<cvm::atom_pos> tmp_reference_fitting_frame_2(reference_fitting_frames[min_frame_index_2].size());
+            for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
+                tmp_reference_fitting_frame_1[i_atom] = reference_fitting_frames[min_frame_index_1][i_atom] - reference_fitting_cog_1;
+                tmp_reference_fitting_frame_2[i_atom] = reference_fitting_frames[min_frame_index_2][i_atom] - reference_fitting_cog_2;
+            }
+            rot_v3.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_2);
+        } else {
+            rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_2);
+        }
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            v3[i_atom] = rot_v3.q.rotate(tmp_reference_frame_1[i_atom]) - tmp_reference_frame_2[i_atom];
+        }
+    } else {
+        cvm::atom_pos reference_cog_1, reference_cog_3;
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            reference_cog_1 += reference_frames[min_frame_index_1][i_atom];
+            reference_cog_3 += reference_frames[min_frame_index_3][i_atom];
+        }
+        reference_cog_1 /= reference_frames[min_frame_index_1].size();
+        reference_cog_3 /= reference_frames[min_frame_index_3].size();
+        std::vector<cvm::atom_pos> tmp_reference_frame_1(reference_frames[min_frame_index_1].size());
+        std::vector<cvm::atom_pos> tmp_reference_frame_3(reference_frames[min_frame_index_3].size());
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            tmp_reference_frame_1[i_atom] = reference_frames[min_frame_index_1][i_atom] - reference_cog_1;
+            tmp_reference_frame_3[i_atom] = reference_frames[min_frame_index_3][i_atom] - reference_cog_3;
+        }
+        if (has_user_defined_fitting) {
+            cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_3;
+            for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
+                reference_fitting_cog_1 += reference_fitting_frames[min_frame_index_1][i_atom];
+                reference_fitting_cog_3 += reference_fitting_frames[min_frame_index_3][i_atom];
+            }
+            reference_fitting_cog_1 /= reference_fitting_frames[min_frame_index_1].size();
+            reference_fitting_cog_3 /= reference_fitting_frames[min_frame_index_3].size();
+            std::vector<cvm::atom_pos> tmp_reference_fitting_frame_1(reference_fitting_frames[min_frame_index_1].size());
+            std::vector<cvm::atom_pos> tmp_reference_fitting_frame_3(reference_fitting_frames[min_frame_index_3].size());
+            for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
+                tmp_reference_fitting_frame_1[i_atom] = reference_fitting_frames[min_frame_index_1][i_atom] - reference_fitting_cog_1;
+                tmp_reference_fitting_frame_3[i_atom] = reference_fitting_frames[min_frame_index_3][i_atom] - reference_fitting_cog_3;
+            }
+            rot_v3.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_3);
+        } else {
+            rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_3);
+        }
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            // v3 = s_(m+1) - s_m
+            v3[i_atom] = tmp_reference_frame_3[i_atom] - rot_v3.q.rotate(tmp_reference_frame_1[i_atom]);
+        }
+    }
+}
+
+void colvar::gspath::calc_value() {
+    computeValue();
+    x = s;
+}
+
+void colvar::gspath::calc_gradients() {
+    computeDerivatives();
+    cvm::rvector tmp_atom_grad_v1, tmp_atom_grad_v2;
+    // dS(v1, v2(r), v3) / dr = ∂S/∂v1 * dv1/dr + ∂S/∂v2 * dv2/dr
+    // dv1/dr = [fitting matrix 1][-1, ..., -1]
+    // dv2/dr = [fitting matrix 2][1, ..., 1]
+    // ∂S/∂v1 = ± (∂f/∂v1) / (2M)
+    // ∂S/∂v2 = ± (∂f/∂v2) / (2M)
+    // dS(v1, v2(r), v3) / dr = -1.0 * ± (∂f/∂v1) / (2M) + ± (∂f/∂v2) / (2M)
+    for (size_t i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+        tmp_atom_grad_v1[0] = -1.0 * sign * 0.5 * dfdv1[i_atom][0] / M;
+        tmp_atom_grad_v1[1] = -1.0 * sign * 0.5 * dfdv1[i_atom][1] / M;
+        tmp_atom_grad_v1[2] = -1.0 * sign * 0.5 * dfdv1[i_atom][2] / M;
+        tmp_atom_grad_v2[0] = sign * 0.5 * dfdv2[i_atom][0] / M;
+        tmp_atom_grad_v2[1] = sign * 0.5 * dfdv2[i_atom][1] / M;
+        tmp_atom_grad_v2[2] = sign * 0.5 * dfdv2[i_atom][2] / M;
+        (*(comp_atoms[min_frame_index_1]))[i_atom].grad += tmp_atom_grad_v1;
+        (*(comp_atoms[min_frame_index_2]))[i_atom].grad += tmp_atom_grad_v2;
+    }
+}
+
+void colvar::gspath::apply_force(colvarvalue const &force) {
+    // The force applied to this CV is scalar type
+    cvm::real const &F = force.real_value;
+    (*(comp_atoms[min_frame_index_1])).apply_colvar_force(F);
+    (*(comp_atoms[min_frame_index_2])).apply_colvar_force(F);
+}
+
+colvar::gzpath::gzpath(std::string const &conf): CartesianBasedPath(conf) {
+    function_type = "gzpath";
+    get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
+    if (use_second_closest_frame == true) {
+        cvm::log(std::string("Geometric path z(σ) will use the second closest frame to compute s_(m-1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m-1)\n"));
+    }
+    get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false);
+    if (use_third_closest_frame == true) {
+        cvm::log(std::string("Geometric path z(σ) will use the third closest frame to compute s_(m+1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m+1)\n"));
+    }
+    bool b_use_z_square = false;
+    get_keyval(conf, "useZsquare", b_use_z_square, false);
+    if (b_use_z_square == true) {
+        cvm::log(std::string("Geometric path z(σ) will use the square of distance from current frame to path compute z\n"));
+    }
+    GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::Z>::initialize(atoms->size(), cvm::atom_pos(), total_reference_frames, use_second_closest_frame, use_third_closest_frame, b_use_z_square);
+    // Logging
+    cvm::log(std::string("Geometric pathCV(z) is initialized.\n"));
+    cvm::log(std::string("Geometric pathCV(z) loaded ") + cvm::to_str(reference_frames.size()) + std::string(" frames.\n"));
+}
+
+void colvar::gzpath::updateReferenceDistances() {
+    computeReferenceDistance(frame_distances);
+}
+
+void colvar::gzpath::prepareVectors() {
+    cvm::atom_pos reference_cog_1, reference_cog_2;
+    size_t i_atom;
+    for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+        reference_cog_1 += reference_frames[min_frame_index_1][i_atom];
+        reference_cog_2 += reference_frames[min_frame_index_2][i_atom];
+    }
+    reference_cog_1 /= reference_frames[min_frame_index_1].size();
+    reference_cog_2 /= reference_frames[min_frame_index_2].size();
+    std::vector<cvm::atom_pos> tmp_reference_frame_1(reference_frames[min_frame_index_1].size());
+    std::vector<cvm::atom_pos> tmp_reference_frame_2(reference_frames[min_frame_index_2].size());
+    for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+        tmp_reference_frame_1[i_atom] = reference_frames[min_frame_index_1][i_atom] - reference_cog_1;
+        tmp_reference_frame_2[i_atom] = reference_frames[min_frame_index_2][i_atom] - reference_cog_2;
+    }
+    std::vector<cvm::atom_pos> tmp_reference_fitting_frame_1;
+    std::vector<cvm::atom_pos> tmp_reference_fitting_frame_2;
+    if (has_user_defined_fitting) {
+        cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_2;
+        for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
+            reference_fitting_cog_1 += reference_fitting_frames[min_frame_index_1][i_atom];
+            reference_fitting_cog_2 += reference_fitting_frames[min_frame_index_2][i_atom];
+        }
+        reference_fitting_cog_1 /= reference_fitting_frames[min_frame_index_1].size();
+        reference_fitting_cog_2 /= reference_fitting_frames[min_frame_index_2].size();
+        tmp_reference_fitting_frame_1.resize(reference_fitting_frames[min_frame_index_1].size());
+        tmp_reference_fitting_frame_2.resize(reference_fitting_frames[min_frame_index_2].size());
+        for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
+            tmp_reference_fitting_frame_1[i_atom] = reference_fitting_frames[min_frame_index_1][i_atom] - reference_fitting_cog_1;
+            tmp_reference_fitting_frame_2[i_atom] = reference_fitting_frames[min_frame_index_2][i_atom] - reference_fitting_cog_2;
+        }
+        rot_v4.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_2);
+    } else {
+        rot_v4.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_2);
+    }
+    for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+        v1[i_atom] = reference_frames[min_frame_index_1][i_atom] - (*(comp_atoms[min_frame_index_1]))[i_atom].pos;
+        v2[i_atom] = (*(comp_atoms[min_frame_index_2]))[i_atom].pos - reference_frames[min_frame_index_2][i_atom];
+        // v4 only computes in gzpath
+        // v4 = s_m - s_(m-1)
+        v4[i_atom] = rot_v4.q.rotate(tmp_reference_frame_1[i_atom]) - tmp_reference_frame_2[i_atom];
+    }
+    if (min_frame_index_3 < 0 || min_frame_index_3 > M) {
+        v3 = v4;
+    } else {
+        cvm::atom_pos reference_cog_3;
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            reference_cog_3 += reference_frames[min_frame_index_3][i_atom];
+        }
+        reference_cog_3 /= reference_frames[min_frame_index_3].size();
+        std::vector<cvm::atom_pos> tmp_reference_frame_3(reference_frames[min_frame_index_3].size());
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            tmp_reference_frame_3[i_atom] = reference_frames[min_frame_index_3][i_atom] - reference_cog_3;
+        }
+        if (has_user_defined_fitting) {
+            cvm::atom_pos reference_fitting_cog_3;
+            for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_3].size(); ++i_atom) {
+                reference_fitting_cog_3 += reference_fitting_frames[min_frame_index_3][i_atom];
+            }
+            reference_fitting_cog_3 /= reference_fitting_frames[min_frame_index_3].size();
+            std::vector<cvm::atom_pos> tmp_reference_fitting_frame_3(reference_fitting_frames[min_frame_index_3].size());
+            for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_3].size(); ++i_atom) {
+                tmp_reference_fitting_frame_3[i_atom] =  reference_fitting_frames[min_frame_index_3][i_atom] - reference_fitting_cog_3;
+            }
+            rot_v3.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_3);
+        } else {
+            rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_3);
+        }
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            // v3 = s_(m+1) - s_m
+            v3[i_atom] = tmp_reference_frame_3[i_atom] - rot_v3.q.rotate(tmp_reference_frame_1[i_atom]);
+        }
+    }
+}
+
+void colvar::gzpath::calc_value() {
+    computeValue();
+    x = z;
+}
+
+void colvar::gzpath::calc_gradients() {
+    computeDerivatives();
+    cvm::rvector tmp_atom_grad_v1, tmp_atom_grad_v2;
+    for (size_t i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+        tmp_atom_grad_v1 = -1.0 * dzdv1[i_atom];
+        tmp_atom_grad_v2 = dzdv2[i_atom];
+        (*(comp_atoms[min_frame_index_1]))[i_atom].grad += tmp_atom_grad_v1;
+        (*(comp_atoms[min_frame_index_2]))[i_atom].grad += tmp_atom_grad_v2;
+    }
+}
+
+void colvar::gzpath::apply_force(colvarvalue const &force) {
+    // The force applied to this CV is scalar type
+    cvm::real const &F = force.real_value;
+    (*(comp_atoms[min_frame_index_1])).apply_colvar_force(F);
+    (*(comp_atoms[min_frame_index_2])).apply_colvar_force(F);
+}
+
+colvar::linearCombination::linearCombination(std::string const &conf): cvc(conf) {
+    GeometricPathCV::init_string_cv_map(string_cv_map);
+    // Lookup all available sub-cvcs
+    for (auto it_cv_map = string_cv_map.begin(); it_cv_map != string_cv_map.end(); ++it_cv_map) {
+        if (key_lookup(conf, it_cv_map->first.c_str())) {
+            std::vector<std::string> sub_cvc_confs;
+            get_key_string_multi_value(conf, it_cv_map->first.c_str(), sub_cvc_confs);
+            for (auto it_sub_cvc_conf = sub_cvc_confs.begin(); it_sub_cvc_conf != sub_cvc_confs.end(); ++it_sub_cvc_conf) {
+                cv.push_back((it_cv_map->second)(*(it_sub_cvc_conf)));
+            }
+        }
+    }
+    // Sort all sub CVs by their names
+    std::sort(cv.begin(), cv.end(), compareColvarComponent);
+    for (auto it_sub_cv = cv.begin(); it_sub_cv != cv.end(); ++it_sub_cv) {
+        for (auto it_atom_group = (*it_sub_cv)->atom_groups.begin(); it_atom_group != (*it_sub_cv)->atom_groups.end(); ++it_atom_group) {
+            register_atom_group(*it_atom_group);
+        }
+    }
+    x.type(cv[0]->value());
+    x.reset();
+    use_explicit_gradients = true;
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
+            use_explicit_gradients = false;
+        }
+    }
+    if (!use_explicit_gradients) {
+        disable(f_cvc_explicit_gradient);
+    }
+}
+
+cvm::real colvar::linearCombination::getPolynomialFactorOfCVGradient(size_t i_cv) const {
+    cvm::real factor_polynomial = 1.0;
+    if (cv[i_cv]->value().type() == colvarvalue::type_scalar) {
+        factor_polynomial = cv[i_cv]->sup_coeff * cv[i_cv]->sup_np * cvm::pow(cv[i_cv]->value().real_value, cv[i_cv]->sup_np - 1);
+    } else {
+        factor_polynomial = cv[i_cv]->sup_coeff;
+    }
+    return factor_polynomial;
+}
+
+colvar::linearCombination::~linearCombination() {
+    for (auto it = cv.begin(); it != cv.end(); ++it) {
+        delete (*it);
+    }
+}
+
+void colvar::linearCombination::calc_value() {
+    x.reset();
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        cv[i_cv]->calc_value();
+        colvarvalue current_cv_value(cv[i_cv]->value());
+        // polynomial combination allowed
+        if (current_cv_value.type() == colvarvalue::type_scalar) {
+            x += cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np));
+        } else {
+            x += cv[i_cv]->sup_coeff * current_cv_value;
+        }
+    }
+}
+
+void colvar::linearCombination::calc_gradients() {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        cv[i_cv]->calc_gradients();
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
+                for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                    for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) {
+                        (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = factor_polynomial * (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad;
+                    }
+                }
+            }
+        }
+    }
+}
+
+void colvar::linearCombination::apply_force(colvarvalue const &force) {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // If this CV us explicit gradients, then atomic gradients is already calculated
+        // We can apply the force to atom groups directly
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)
+        ) {
+            for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                (cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value);
+            }
+        } else {
+            // Compute factors for polynomial combinations
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            colvarvalue cv_force = force.real_value * factor_polynomial;
+            cv[i_cv]->apply_force(cv_force);
+        }
+    }
+}
+
+colvar::CVBasedPath::CVBasedPath(std::string const &conf): cvc(conf) {
+    GeometricPathCV::init_string_cv_map(string_cv_map);
+    // Lookup all available sub-cvcs
+    for (auto it_cv_map = string_cv_map.begin(); it_cv_map != string_cv_map.end(); ++it_cv_map) {
+        if (key_lookup(conf, it_cv_map->first.c_str())) {
+            std::vector<std::string> sub_cvc_confs;
+            get_key_string_multi_value(conf, it_cv_map->first.c_str(), sub_cvc_confs);
+            for (auto it_sub_cvc_conf = sub_cvc_confs.begin(); it_sub_cvc_conf != sub_cvc_confs.end(); ++it_sub_cvc_conf) {
+                cv.push_back((it_cv_map->second)(*(it_sub_cvc_conf)));
+            }
+        }
+    }
+    // Sort all sub CVs by their names
+    std::sort(cv.begin(), cv.end(), compareColvarComponent);
+    // Register atom groups and determine the colvar type for reference
+    std::vector<colvarvalue> tmp_cv;
+    for (auto it_sub_cv = cv.begin(); it_sub_cv != cv.end(); ++it_sub_cv) {
+        for (auto it_atom_group = (*it_sub_cv)->atom_groups.begin(); it_atom_group != (*it_sub_cv)->atom_groups.end(); ++it_atom_group) {
+            register_atom_group(*it_atom_group);
+        }
+        colvarvalue tmp_i_cv((*it_sub_cv)->value());
+        tmp_i_cv.reset();
+        tmp_cv.push_back(tmp_i_cv);
+    }
+    // Read path file
+    // Lookup all reference CV values
+    std::string path_filename;
+    get_keyval(conf, "pathFile", path_filename);
+    cvm::log(std::string("Reading path file: ") + path_filename + std::string("\n"));
+    std::ifstream ifs_path(path_filename);
+    if (!ifs_path.is_open()) {
+        cvm::error("Error: failed to open path file.\n");
+    }
+    std::string line;
+    const std::string token(" ");
+    total_reference_frames = 0;
+    while (std::getline(ifs_path, line)) {
+        std::vector<std::string> fields;
+        split_string(line, token, fields);
+        size_t num_value_required = 0;
+        for (size_t i_cv = 0; i_cv < tmp_cv.size(); ++i_cv) {
+            const size_t value_size = tmp_cv[i_cv].size();
+            num_value_required += value_size;
+            cvm::log(std::string("Reading CV ") + cv[i_cv]->name + std::string(" with ") + cvm::to_str(value_size) + std::string(" value(s)\n"));
+            if (num_value_required <= fields.size()) {
+                size_t start_index = num_value_required - value_size;
+                for (size_t i = start_index; i < num_value_required; ++i) {
+                    tmp_cv[i_cv][i] = std::atof(fields[i].c_str());
+                    cvm::log(fields[i] + std::string(" "));
+                }
+                cvm::log(std::string("\n"));
+            } else {
+                cvm::error("Error: incorrect format of path file.\n");
+            }
+        }
+        if (!fields.empty()) {
+            ref_cv.push_back(tmp_cv);
+            ++total_reference_frames;
+        }
+    }
+    x.type(colvarvalue::type_scalar);
+    use_explicit_gradients = true;
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
+            use_explicit_gradients = false;
+        }
+    }
+    if (!use_explicit_gradients) {
+        disable(f_cvc_explicit_gradient);
+    }
+}
+
+void colvar::CVBasedPath::computeReferenceDistance(std::vector<cvm::real>& result) {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        cv[i_cv]->calc_value();
+    }
+    for (size_t i_frame = 0; i_frame < ref_cv.size(); ++i_frame) {
+        cvm::real rmsd_i = 0.0;
+        for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+            colvarvalue ref_cv_value(ref_cv[i_frame][i_cv]);
+            colvarvalue current_cv_value(cv[i_cv]->value());
+            // polynomial combination allowed
+            if (current_cv_value.type() == colvarvalue::type_scalar) {
+                // wrapping is already in dist2
+                rmsd_i += cv[i_cv]->dist2(cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)), ref_cv_value.real_value);
+            } else {
+                rmsd_i += cv[i_cv]->dist2(cv[i_cv]->sup_coeff * current_cv_value, ref_cv_value);
+            }
+        }
+        rmsd_i /= cvm::real(cv.size());
+        rmsd_i = cvm::sqrt(rmsd_i);
+        result[i_frame] = rmsd_i;
+    }
+}
+
+cvm::real colvar::CVBasedPath::getPolynomialFactorOfCVGradient(size_t i_cv) const {
+    cvm::real factor_polynomial = 1.0;
+    if (cv[i_cv]->value().type() == colvarvalue::type_scalar) {
+        factor_polynomial = cv[i_cv]->sup_coeff * cv[i_cv]->sup_np * cvm::pow(cv[i_cv]->value().real_value, cv[i_cv]->sup_np - 1);
+    } else {
+        factor_polynomial = cv[i_cv]->sup_coeff;
+    }
+    return factor_polynomial;
+}
+
+colvar::CVBasedPath::~CVBasedPath() {
+    for (auto it = cv.begin(); it != cv.end(); ++it) {
+        delete (*it);
+    }
+}
+
+colvar::gspathCV::gspathCV(std::string const &conf): CVBasedPath(conf) {
+    function_type = "gspathCV";
+    cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
+    // Initialize variables for future calculation
+    get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
+    if (use_second_closest_frame == true) {
+        cvm::log(std::string("Geometric path s(σ) will use the second closest frame to compute s_(m-1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m-1)\n"));
+    }
+    get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false);
+    if (use_third_closest_frame == true) {
+        cvm::log(std::string("Geometric path s(σ) will use the third closest frame to compute s_(m+1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m+1)\n"));
+    }
+    GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::S>::initialize(cv.size(), ref_cv[0], total_reference_frames, use_second_closest_frame, use_third_closest_frame);
+    x.type(colvarvalue::type_scalar);
+    use_explicit_gradients = true;
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
+            use_explicit_gradients = false;
+        }
+    }
+    if (!use_explicit_gradients) {
+        cvm::log("Geometric path s(σ) will use implicit gradients.\n");
+        disable(f_cvc_explicit_gradient);
+    }
+}
+
+colvar::gspathCV::~gspathCV() {}
+
+void colvar::gspathCV::updateReferenceDistances() {
+    computeReferenceDistance(frame_distances);
+}
+
+void colvar::gspathCV::prepareVectors() {
+    // Compute v1, v2 and v3
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // values of sub-cvc are computed in update_distances
+        // cv[i_cv]->calc_value();
+        colvarvalue f1_ref_cv_i_value(ref_cv[min_frame_index_1][i_cv]);
+        colvarvalue f2_ref_cv_i_value(ref_cv[min_frame_index_2][i_cv]);
+        colvarvalue current_cv_value(cv[i_cv]->value());
+        // polynomial combination allowed
+        if (current_cv_value.type() == colvarvalue::type_scalar) {
+            v1[i_cv] = f1_ref_cv_i_value.real_value - cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np));
+            v2[i_cv] = cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)) - f2_ref_cv_i_value.real_value;
+        } else {
+            v1[i_cv] = f1_ref_cv_i_value - cv[i_cv]->sup_coeff * current_cv_value;
+            v2[i_cv] = cv[i_cv]->sup_coeff * current_cv_value - f2_ref_cv_i_value;
+        }
+        cv[i_cv]->wrap(v1[i_cv]);
+        cv[i_cv]->wrap(v2[i_cv]);
+    }
+    if (min_frame_index_3 < 0 || min_frame_index_3 > M) {
+        for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+            v3[i_cv] = ref_cv[min_frame_index_1][i_cv] - ref_cv[min_frame_index_2][i_cv];
+            cv[i_cv]->wrap(v3[i_cv]);
+        }
+    } else {
+        for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+            v3[i_cv] = ref_cv[min_frame_index_3][i_cv] - ref_cv[min_frame_index_1][i_cv];
+            cv[i_cv]->wrap(v3[i_cv]);
+        }
+    }
+}
+
+void colvar::gspathCV::calc_value() {
+    computeValue();
+    x = s;
+}
+
+void colvar::gspathCV::calc_gradients() {
+    computeDerivatives();
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // No matter whether the i-th cv uses implicit gradient, compute it first.
+        cv[i_cv]->calc_gradients();
+        // If the gradient is not implicit, then add the gradients to its atom groups
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
+            // Temporary variables storing gradients
+            colvarvalue tmp_cv_grad_v1(cv[i_cv]->value());
+            colvarvalue tmp_cv_grad_v2(cv[i_cv]->value());
+            // Compute factors for polynomial combinations
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            // Loop over all elements of the corresponding colvar value
+            for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
+                // ds/dz, z = vector of CVs
+                tmp_cv_grad_v1[j_elem] = -1.0 * sign * 0.5 * dfdv1[i_cv][j_elem] / M;
+                tmp_cv_grad_v2[j_elem] = sign * 0.5 * dfdv2[i_cv][j_elem] / M;
+                // Apply the gradients to the atom groups in i-th cv
+                // Loop over all atom groups
+                for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                    // Loop over all atoms in the k-th atom group
+                    for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) {
+                        // Chain rule
+                        (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = factor_polynomial * ((*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v1[j_elem] + (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v2[j_elem]);
+                    }
+                }
+            }
+        }
+    }
+}
+
+void colvar::gspathCV::apply_force(colvarvalue const &force) {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // If this CV us explicit gradients, then atomic gradients is already calculated
+        // We can apply the force to atom groups directly
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)
+        ) {
+            for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                (cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value);
+            }
+        } else {
+            // Temporary variables storing gradients
+            colvarvalue tmp_cv_grad_v1(cv[i_cv]->value());
+            colvarvalue tmp_cv_grad_v2(cv[i_cv]->value());
+            // Compute factors for polynomial combinations
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
+                // ds/dz, z = vector of CVs
+                tmp_cv_grad_v1[j_elem] = -1.0 * sign * 0.5 * dfdv1[i_cv][j_elem] / M;
+                tmp_cv_grad_v2[j_elem] = sign * 0.5 * dfdv2[i_cv][j_elem] / M;
+            }
+            colvarvalue cv_force = force.real_value * factor_polynomial * (tmp_cv_grad_v1 + tmp_cv_grad_v2);
+            cv[i_cv]->apply_force(cv_force);
+        }
+    }
+}
+
+colvar::gzpathCV::gzpathCV(std::string const &conf): CVBasedPath(conf) {
+    function_type = "gzpathCV";
+    cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
+    // Initialize variables for future calculation
+    M = cvm::real(total_reference_frames - 1);
+    m = 1.0;
+    get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
+    if (use_second_closest_frame == true) {
+        cvm::log(std::string("Geometric path z(σ) will use the second closest frame to compute s_(m-1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m-1)\n"));
+    }
+    get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false);
+    if (use_third_closest_frame == true) {
+        cvm::log(std::string("Geometric path z(σ) will use the third closest frame to compute s_(m+1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m+1)\n"));
+    }
+    bool b_use_z_square = false;
+    get_keyval(conf, "useZsquare", b_use_z_square, false);
+    if (b_use_z_square == true) {
+        cvm::log(std::string("Geometric path z(σ) will use the square of distance from current frame to path compute z\n"));
+    }
+    GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::Z>::initialize(cv.size(), ref_cv[0], total_reference_frames, use_second_closest_frame, use_third_closest_frame, b_use_z_square);
+    x.type(colvarvalue::type_scalar);
+    use_explicit_gradients = true;
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
+            use_explicit_gradients = false;
+        }
+    }
+    if (!use_explicit_gradients) {
+        cvm::log("Geometric path z(σ) will use implicit gradients.\n");
+        disable(f_cvc_explicit_gradient);
+    }
+}
+
+colvar::gzpathCV::~gzpathCV() {
+}
+
+void colvar::gzpathCV::updateReferenceDistances() {
+    computeReferenceDistance(frame_distances);
+}
+
+void colvar::gzpathCV::prepareVectors() {
+    // Compute v1, v2 and v3
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // values of sub-cvc are computed in update_distances
+        // cv[i_cv]->calc_value();
+        colvarvalue f1_ref_cv_i_value(ref_cv[min_frame_index_1][i_cv]);
+        colvarvalue f2_ref_cv_i_value(ref_cv[min_frame_index_2][i_cv]);
+        colvarvalue current_cv_value(cv[i_cv]->value());
+        // polynomial combination allowed
+        if (current_cv_value.type() == colvarvalue::type_scalar) {
+            v1[i_cv] = f1_ref_cv_i_value.real_value - cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np));
+            v2[i_cv] = cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)) - f2_ref_cv_i_value.real_value;
+        } else {
+            v1[i_cv] = f1_ref_cv_i_value - cv[i_cv]->sup_coeff * current_cv_value;
+            v2[i_cv] = cv[i_cv]->sup_coeff * current_cv_value - f2_ref_cv_i_value;
+        }
+        v4[i_cv] = f1_ref_cv_i_value - f2_ref_cv_i_value;
+        cv[i_cv]->wrap(v1[i_cv]);
+        cv[i_cv]->wrap(v2[i_cv]);
+        cv[i_cv]->wrap(v4[i_cv]);
+    }
+    if (min_frame_index_3 < 0 || min_frame_index_3 > M) {
+        for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+            v3[i_cv] = ref_cv[min_frame_index_1][i_cv] - ref_cv[min_frame_index_2][i_cv];
+            cv[i_cv]->wrap(v3[i_cv]);
+        }
+    } else {
+        for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+            v3[i_cv] = ref_cv[min_frame_index_3][i_cv] - ref_cv[min_frame_index_1][i_cv];
+            cv[i_cv]->wrap(v3[i_cv]);
+        }
+    }
+}
+
+void colvar::gzpathCV::calc_value() {
+    computeValue();
+    x = z;
+}
+
+void colvar::gzpathCV::calc_gradients() {
+    computeDerivatives();
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // No matter whether the i-th cv uses implicit gradient, compute it first.
+        cv[i_cv]->calc_gradients();
+        // If the gradient is not implicit, then add the gradients to its atom groups
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
+            // Temporary variables storing gradients
+            colvarvalue tmp_cv_grad_v1 = -1.0 * dzdv1[i_cv];
+            colvarvalue tmp_cv_grad_v2 =  1.0 * dzdv2[i_cv];
+            // Compute factors for polynomial combinations
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
+                // Apply the gradients to the atom groups in i-th cv
+                // Loop over all atom groups
+                for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                    // Loop over all atoms in the k-th atom group
+                    for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) {
+                        // Chain rule
+                        (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = factor_polynomial * ((*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v1[j_elem] + (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v2[j_elem]);
+                    }
+                }
+            }
+        }
+    }
+}
+
+void colvar::gzpathCV::apply_force(colvarvalue const &force) {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // If this CV us explicit gradients, then atomic gradients is already calculated
+        // We can apply the force to atom groups directly
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
+            for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                (cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value);
+            }
+        }
+        else {
+            colvarvalue tmp_cv_grad_v1 = -1.0 * dzdv1[i_cv];
+            colvarvalue tmp_cv_grad_v2 =  1.0 * dzdv2[i_cv];
+            // Temporary variables storing gradients
+            // Compute factors for polynomial combinations
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            colvarvalue cv_force = force.real_value * factor_polynomial * (tmp_cv_grad_v1 + tmp_cv_grad_v2);
+            cv[i_cv]->apply_force(cv_force);
+        }
+    }
+}
+
+void GeometricPathCV::init_string_cv_map(std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>>& string_cv_map) {
+    string_cv_map["distance"]              = [](const std::string& conf){return new colvar::distance(conf);};
+    string_cv_map["dihedral"]              = [](const std::string& conf){return new colvar::dihedral(conf);};
+    string_cv_map["angle"]                 = [](const std::string& conf){return new colvar::angle(conf);};
+    string_cv_map["rmsd"]                  = [](const std::string& conf){return new colvar::rmsd(conf);};
+    string_cv_map["gyration"]              = [](const std::string& conf){return new colvar::gyration(conf);};
+    string_cv_map["inertia"]               = [](const std::string& conf){return new colvar::inertia(conf);};
+    string_cv_map["inertiaZ"]              = [](const std::string& conf){return new colvar::inertia_z(conf);};
+    string_cv_map["tilt"]                  = [](const std::string& conf){return new colvar::tilt(conf);};
+    string_cv_map["distanceZ"]             = [](const std::string& conf){return new colvar::distance_z(conf);};
+    string_cv_map["distanceXY"]            = [](const std::string& conf){return new colvar::distance_xy(conf);};
+    string_cv_map["polarTheta"]            = [](const std::string& conf){return new colvar::polar_theta(conf);};
+    string_cv_map["polarPhi"]              = [](const std::string& conf){return new colvar::polar_phi(conf);};
+    string_cv_map["distanceVec"]           = [](const std::string& conf){return new colvar::distance_vec(conf);};
+    string_cv_map["orientationAngle"]      = [](const std::string& conf){return new colvar::orientation_angle(conf);};
+    string_cv_map["distancePairs"]         = [](const std::string& conf){return new colvar::distance_pairs(conf);};
+    string_cv_map["dipoleMagnitude"]       = [](const std::string& conf){return new colvar::dipole_magnitude(conf);};
+    string_cv_map["coordNum"]              = [](const std::string& conf){return new colvar::coordnum(conf);};
+    string_cv_map["selfCoordNum"]          = [](const std::string& conf){return new colvar::selfcoordnum(conf);};
+    string_cv_map["dipoleAngle"]           = [](const std::string& conf){return new colvar::dipole_angle(conf);};
+    string_cv_map["orientation"]           = [](const std::string& conf){return new colvar::orientation(conf);};
+    string_cv_map["orientationProj"]       = [](const std::string& conf){return new colvar::orientation_proj(conf);};
+    string_cv_map["eigenvector"]           = [](const std::string& conf){return new colvar::eigenvector(conf);};
+    string_cv_map["cartesian"]             = [](const std::string& conf){return new colvar::cartesian(conf);};
+    string_cv_map["alpha"]                 = [](const std::string& conf){return new colvar::alpha_angles(conf);};
+    string_cv_map["dihedralPC"]            = [](const std::string& conf){return new colvar::dihedPC(conf);};
+    string_cv_map["linearCombination"]     = [](const std::string& conf){return new colvar::linearCombination(conf);};
+}
+
+#endif
diff --git a/lib/colvars/colvarcomp_protein.cpp b/lib/colvars/colvarcomp_protein.cpp
index b9f9c60cdb..aa61cdf1dc 100644
--- a/lib/colvars/colvarcomp_protein.cpp
+++ b/lib/colvars/colvarcomp_protein.cpp
@@ -7,6 +7,8 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
+#include <algorithm>
+
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvarparse.h"
diff --git a/lib/colvars/colvargrid.cpp b/lib/colvars/colvargrid.cpp
index dc1a709edb..bc5ac3c57c 100644
--- a/lib/colvars/colvargrid.cpp
+++ b/lib/colvars/colvargrid.cpp
@@ -109,7 +109,9 @@ cvm::real colvar_grid_scalar::entropy() const
 {
   cvm::real sum = 0.0;
   for (size_t i = 0; i < nt; i++) {
-    sum += -1.0 * data[i] * cvm::logn(data[i]);
+    if (data[i] >0) {
+      sum += -1.0 * data[i] * cvm::logn(data[i]);
+    }
   }
   cvm::real bin_volume = 1.0;
   for (size_t id = 0; id < widths.size(); id++) {
diff --git a/lib/colvars/colvargrid.h b/lib/colvars/colvargrid.h
index 2ba0566e49..7792b7d0df 100644
--- a/lib/colvars/colvargrid.h
+++ b/lib/colvars/colvargrid.h
@@ -557,11 +557,11 @@ public:
       data[i] *= a;
   }
 
-  /// \brief Assign all zero elements a scalar constant (fast loop)
-  inline void remove_zeros(cvm::real const &a)
+  /// \brief Assign values that are smaller than scalar constant the latter value (fast loop)
+  inline void remove_small_values(cvm::real const &a)
   {
     for (size_t i = 0; i < nt; i++)
-      if(data[i]==0) data[i] = a;
+      if(data[i]<a) data[i] = a;
   }
 
 
diff --git a/lib/colvars/colvarparse.cpp b/lib/colvars/colvarparse.cpp
index 10dce911ee..8041153494 100644
--- a/lib/colvars/colvarparse.cpp
+++ b/lib/colvars/colvarparse.cpp
@@ -7,7 +7,6 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
-
 #include <sstream>
 #include <iostream>
 #include <algorithm>
@@ -58,6 +57,28 @@ bool colvarparse::get_key_string_value(std::string const &conf,
   return b_found_any;
 }
 
+bool colvarparse::get_key_string_multi_value(std::string const &conf,
+                                             char const *key, std::vector<std::string>& data)
+{
+  bool b_found = false, b_found_any = false;
+  size_t save_pos = 0, found_count = 0;
+
+  data.clear();
+
+  do {
+    std::string data_this = "";
+    b_found = key_lookup(conf, key, &data_this, &save_pos);
+    if (b_found) {
+      if (!b_found_any)
+        b_found_any = true;
+      found_count++;
+      data.push_back(data_this);
+    }
+  } while (b_found);
+
+  return b_found_any;
+}
+
 
 template<typename TYPE>
 void colvarparse::mark_key_set_user(std::string const &key_str,
@@ -843,3 +864,18 @@ int colvarparse::check_braces(std::string const &conf,
   }
   return (brace_count != 0) ? INPUT_ERROR : COLVARS_OK;
 }
+
+void colvarparse::split_string(const std::string& data, const std::string& delim, std::vector<std::string>& dest) {
+    size_t index = 0, new_index = 0;
+    std::string tmpstr;
+    while (index != data.length()) {
+        new_index = data.find(delim, index);
+        if (new_index != std::string::npos) tmpstr = data.substr(index, new_index - index);
+        else tmpstr = data.substr(index, data.length());
+        if (!tmpstr.empty()) {
+            dest.push_back(tmpstr);
+        }
+        if (new_index == std::string::npos) break;
+        index = new_index + 1;
+    }
+}
diff --git a/lib/colvars/colvarparse.h b/lib/colvars/colvarparse.h
index 8501ee8c14..f4ead26601 100644
--- a/lib/colvars/colvarparse.h
+++ b/lib/colvars/colvarparse.h
@@ -212,6 +212,10 @@ protected:
   bool get_key_string_value(std::string const &conf,
                             char const *key, std::string &data);
 
+  /// Get multiple strings from repeated instances of a same keyword
+  bool get_key_string_multi_value(std::string const &conf,
+                                  char const *key, std::vector<std::string>& data);
+
   /// Template for single-value keyword parsers
   template<typename TYPE>
   bool _get_keyval_scalar_(std::string const &conf,
@@ -322,6 +326,12 @@ public:
   /// from this position
   static int check_braces(std::string const &conf, size_t const start_pos);
 
+  /// \brief Split a string with a specified delimiter into a vector
+  /// \param data The string to be splitted
+  /// \param delim A delimiter
+  /// \param dest A destination vector to store the splitted results
+  static void split_string(const std::string& data, const std::string& delim, std::vector<std::string>& dest);
+
 protected:
 
   /// \brief List of legal keywords for this object: this is updated
diff --git a/lib/colvars/colvarproxy.cpp b/lib/colvars/colvarproxy.cpp
index 5f8e82d30a..f077984556 100644
--- a/lib/colvars/colvarproxy.cpp
+++ b/lib/colvars/colvarproxy.cpp
@@ -7,8 +7,14 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
+#if !defined(WIN32) || defined(__CYGWIN__)
+#include <unistd.h>
+#endif
+#include <cerrno>
+
 #include <sstream>
 #include <cstring>
+#include <cstdio>
 
 #if defined(_OPENMP)
 #include <omp.h>
@@ -704,6 +710,27 @@ std::ostream * colvarproxy_io::output_stream(std::string const &output_name,
   if (cvm::debug()) {
     cvm::log("Using colvarproxy::output_stream()\n");
   }
+
+  std::ostream *os = get_output_stream(output_name);
+  if (os != NULL) return os;
+
+  if (!(mode & (std::ios_base::app | std::ios_base::ate))) {
+    backup_file(output_name);
+  }
+  std::ofstream *osf = new std::ofstream(output_name.c_str(), mode);
+  if (!osf->is_open()) {
+    cvm::error("Error: cannot write to file/channel \""+output_name+"\".\n",
+               FILE_ERROR);
+    return NULL;
+  }
+  output_stream_names.push_back(output_name);
+  output_files.push_back(osf);
+  return osf;
+}
+
+
+std::ostream *colvarproxy_io::get_output_stream(std::string const &output_name)
+{
   std::list<std::ostream *>::iterator osi  = output_files.begin();
   std::list<std::string>::iterator    osni = output_stream_names.begin();
   for ( ; osi != output_files.end(); osi++, osni++) {
@@ -711,21 +738,11 @@ std::ostream * colvarproxy_io::output_stream(std::string const &output_name,
       return *osi;
     }
   }
-  if (!(mode & (std::ios_base::app | std::ios_base::ate))) {
-    backup_file(output_name);
-  }
-  std::ofstream *os = new std::ofstream(output_name.c_str(), mode);
-  if (!os->is_open()) {
-    cvm::error("Error: cannot write to file/channel \""+output_name+"\".\n",
-               FILE_ERROR);
-    return NULL;
-  }
-  output_stream_names.push_back(output_name);
-  output_files.push_back(os);
-  return os;
+  return NULL;
 }
 
 
+
 int colvarproxy_io::flush_output_stream(std::ostream *os)
 {
   std::list<std::ostream *>::iterator osi  = output_files.begin();
@@ -761,10 +778,45 @@ int colvarproxy_io::close_output_stream(std::string const &output_name)
 
 int colvarproxy_io::backup_file(char const *filename)
 {
+  // TODO implement this using rename_file()
   return COLVARS_NOT_IMPLEMENTED;
 }
 
 
+int colvarproxy_io::remove_file(char const *filename)
+{
+  if (std::remove(filename)) {
+    if (errno != ENOENT) {
+      return cvm::error("Error: in removing file \""+std::string(filename)+
+                        "\".\n.",
+                        FILE_ERROR);
+    }
+  }
+  return COLVARS_OK;
+}
+
+
+int colvarproxy_io::rename_file(char const *filename, char const *newfilename)
+{
+  int error_code = COLVARS_OK;
+#if defined(WIN32) && !defined(__CYGWIN__)
+  // On straight Windows, must remove the destination before renaming it
+  error_code |= remove_file(newfilename);
+#endif
+  int rename_exit_code = 0;
+  while ((rename_exit_code = std::rename(filename, newfilename)) != 0) {
+    if (errno == EINTR) continue;
+    // Call log() instead of error to allow the next try
+    cvm::log("Error: in renaming file \""+std::string(filename)+"\" to \""+
+             std::string(newfilename)+"\".\n.");
+    error_code |= FILE_ERROR;
+    if (errno == EXDEV) continue;
+    break;
+  }
+  return rename_exit_code ? error_code : COLVARS_OK;
+}
+
+
 
 colvarproxy::colvarproxy()
 {
@@ -826,4 +878,3 @@ int colvarproxy::get_version_from_string(char const *version_string)
   is >> newint;
   return newint;
 }
-
diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h
index 3bbdfe522e..21944106f1 100644
--- a/lib/colvars/colvarproxy.h
+++ b/lib/colvars/colvarproxy.h
@@ -571,7 +571,10 @@ public:
   /// if this is not open already, then open it
   virtual std::ostream *output_stream(std::string const &output_name,
                                       std::ios_base::openmode mode =
-                                        std::ios_base::out);
+                                      std::ios_base::out);
+
+  /// Returns a reference to output_name if it exists, NULL otherwise
+  virtual std::ostream *get_output_stream(std::string const &output_name);
 
   /// \brief Flushes the given output channel
   virtual int flush_output_stream(std::ostream *os);
@@ -588,6 +591,25 @@ public:
     return backup_file(filename.c_str());
   }
 
+  /// Remove the given file
+  int remove_file(char const *filename);
+
+  /// Remove the given file
+  inline int remove_file(std::string const &filename)
+  {
+    return remove_file(filename.c_str());
+  }
+
+  /// Rename the given file
+  int rename_file(char const *filename, char const *newfilename);
+
+  /// Rename the given file
+  inline int rename_file(std::string const &filename,
+                         std::string const &newfilename)
+  {
+    return rename_file(filename.c_str(), newfilename.c_str());
+  }
+
   /// \brief Prefix of the input state file
   inline std::string & input_prefix()
   {
diff --git a/lib/colvars/colvars_version.h b/lib/colvars/colvars_version.h
index 2521fdf872..77b3bd7e38 100644
--- a/lib/colvars/colvars_version.h
+++ b/lib/colvars/colvars_version.h
@@ -1,5 +1,5 @@
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2019-04-26"
+#define COLVARS_VERSION "2019-08-05"
 // This file is part of the Collective Variables module (Colvars).
 // The original version of Colvars and its updates are located at:
 // https://github.com/colvars/colvars
diff --git a/lib/kim/Install.py b/lib/kim/Install.py
index c3588241c4..33d0071dde 100644
--- a/lib/kim/Install.py
+++ b/lib/kim/Install.py
@@ -10,7 +10,7 @@ import sys, os, subprocess, shutil
 from argparse import ArgumentParser
 
 sys.path.append('..')
-from install_helpers import fullpath, geturl
+from install_helpers import fullpath, geturl, checkmd5sum
 
 parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
@@ -18,7 +18,15 @@ parser = ArgumentParser(prog='Install.py',
 # settings
 
 thisdir = fullpath('.')
-version = "kim-api-2.0.2"
+version = "2.1.3"
+
+# known checksums for different KIM-API versions. used to validate the download.
+checksums = { \
+        '2.1.2' : '6ac52e14ef52967fc7858220b208cba5', \
+        '2.1.3' : '6ee829a1bbba5f8b9874c88c4c4ebff8', \
+        }
+
+
 
 # help message
 
@@ -39,11 +47,8 @@ make lib-kim args="-b -a EAM_ErcolessiAdams_1994_Al__MO_324507536345_002" # Ditt
 make lib-kim args="-b -a everything"   # install KIM API lib with all models
 make lib-kim args="-n -a EAM_Dynamo_Ackland_2003_W__MO_141627196590_005"    # only add one model or model driver
 
-See the list of KIM model drivers here:
-https://openkim.org/browse/model-drivers/alphabetical
-
 See the list of all KIM models here:
-https://openkim.org/browse/models/by-model-drivers
+https://openkim.org/browse/models
 """
 
 pgroup = parser.add_mutually_exclusive_group()
@@ -53,7 +58,7 @@ pgroup.add_argument("-n", "--nobuild", action="store_true",
                     help="use the previously downloaded and compiled base KIM API.")
 pgroup.add_argument("-p", "--path",
                     help="specify location of existing KIM API installation.")
-parser.add_argument("-v", "--version", default=version,
+parser.add_argument("-v", "--version", default=version, choices=checksums.keys(),
                     help="set version of KIM API library to download and build (default: %s)" % version)
 parser.add_argument("-a", "--add",
                     help="add single KIM model or model driver. If adding 'everything', then all available OpenKIM models are added (may take a long time)")
@@ -76,6 +81,7 @@ if addflag and addmodelname == "everything":
   everythingflag = True
   buildflag = True
 verboseflag = args.verbose
+version = args.version
 
 if pathflag:
   buildflag = False
@@ -84,7 +90,7 @@ if pathflag:
     sys.exit("KIM API path %s does not exist" % kimdir)
   kimdir = fullpath(kimdir)
 
-url = "https://s3.openkim.org/kim-api/%s.txz" % version
+url = "https://s3.openkim.org/kim-api/kim-api-%s.txz" % version
 
 # set KIM API directory
 
@@ -118,21 +124,28 @@ if buildflag:
   # download entire kim-api tarball
 
   print("Downloading kim-api tarball ...")
-  geturl(url, "%s/%s.txz" % (thisdir, version))
+  filename = "kim-api-%s.txz" % version
+  geturl(url, "%s/%s" % (thisdir, filename))
+
+  # verify downloaded archive integrity via md5 checksum, if known.
+  if version in checksums:
+    if not checkmd5sum(checksums[version], filename):
+      sys.exit("Checksum for KIM-API library does not match")
+
   print("Unpacking kim-api tarball ...")
-  cmd = 'cd "%s"; rm -rf "%s"; tar -xJvf %s.txz' % (thisdir, version, version)
+  cmd = 'cd "%s"; rm -rf "kim-api-%s"; tar -xJvf %s' % (thisdir, version, filename)
   subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
 
   # configure kim-api
 
   print("Configuring kim-api ...")
-  cmd = 'cd "%s/%s" && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX="%s" -DCMAKE_BUILD_TYPE=Release' % (thisdir,version,kimdir)
+  cmd = 'cd "%s/kim-api-%s" && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX="%s" -DCMAKE_BUILD_TYPE=Release' % (thisdir,version,kimdir)
   txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
   if verboseflag: print(txt.decode("UTF-8"))
 
   # build kim-api
   print("Building kim-api ...")
-  cmd = 'cd "%s/%s/build" && make' % (thisdir, version)
+  cmd = 'cd "%s/kim-api-%s/build" && make -j2' % (thisdir, version)
   txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
   if verboseflag:
     print(txt.decode("UTF-8"))
@@ -140,7 +153,7 @@ if buildflag:
   # install kim-api
 
   print("Installing kim-api ...")
-  cmd = 'cd "%s/%s/build" && make install' % (thisdir, version)
+  cmd = 'cd "%s/kim-api-%s/build" && make -j2 install' % (thisdir, version)
   txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
   if verboseflag:
     print(txt.decode("UTF-8"))
@@ -148,7 +161,7 @@ if buildflag:
   # remove source files
 
   print("Removing kim-api source and build files ...")
-  cmd = 'cd "%s"; rm -rf %s; rm -rf %s.txz' % (thisdir, version, version)
+  cmd = 'cd "%s"; rm -rf kim-api-%s; rm -rf kim-api-%s.txz' % (thisdir, version, version)
   subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
 
   # add all OpenKIM models, if desired
diff --git a/lib/kim/README b/lib/kim/README
index d3327537b6..3cba4a4597 100644
--- a/lib/kim/README
+++ b/lib/kim/README
@@ -1,11 +1,11 @@
-This directory contains build settings for the KIM API library which
-is required to use the KIM package and its pair_style kim command in a
-LAMMPS input script.
+This directory contains build settings for the KIM API library which is
+required to use the KIM package and its kim_init, kim_interactions, kim_query,
+and pair_kim commands in a LAMMPS input script.
 
 Information about the KIM project can be found at https://openkim.org.
 The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn).
 Ryan Elliott is the main developer for the KIM API and he also
-maintains the code that implements the pair_style kim command.
+maintains the code that implements the KIM commands.
 
 You can type "make lib-kim" from the src directory to see help on
 how to download and build this library via make commands, or you can
@@ -13,11 +13,9 @@ do the same thing by typing "python Install.py" from within this
 directory, or you can do it manually by following the instructions
 below.
 
-As of KIM API version 2, the KIM package also provides a LAMMPS command
-to perform queries through the OpenKIM web API. This feature requires
-that the CURL library (libcurl) development package and its configuration
-query tool, curl-config, are installed. The provided Makefile.lammps
-is set up to automatically detect this.
+Use of the kim_query command requires that the CURL library (libcurl)
+development package and its configuration query tool, curl-config, are
+installed. The provided Makefile.lammps is set up to automatically detect this.
 
 -----------------
 
@@ -40,8 +38,8 @@ $ cmake ..  -DCMAKE_INSTALL_PREFIX=${PWD}/../../installed-kim-api-X.Y.Z
 
 3. Build and install the kim-api and model
 
-$ make
-$ make install
+$ make -j2
+$ make -j2 install
 
 4. Remove source and build files
 
@@ -53,7 +51,7 @@ $ rm -rf kim-api-X.Y.Z.txz
    desired value)
 
 $ source ${PWD}/kim-api-X.Y.Z/bin/kim-api-activate
-$ kim-api-collections-management install system Pair_Johnson_Fe__MO_857282754307_002
+$ kim-api-collections-management install system EAM_ErcolessiAdams_1994_Al__MO_324507536345_002
 
 
 -----------------
diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py
index 3623a8cff0..d56b68b877 100644
--- a/lib/plumed/Install.py
+++ b/lib/plumed/Install.py
@@ -6,7 +6,7 @@ used to automate the steps described in the README file in this dir
 """
 
 from __future__ import print_function
-import sys, os, subprocess, shutil
+import sys, os, platform, subprocess, shutil
 from argparse import ArgumentParser
 
 sys.path.append('..')
@@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py',
 
 # settings
 
-version = "2.5.1"
+version = "2.5.2"
 mode = "static"
 
 # help message
@@ -44,6 +44,7 @@ checksums = { \
         '2.4.4' : '71ed465bdc7c2059e282dbda8d564e71', \
         '2.5.0' : '6224cd089493661e19ceacccd35cf911', \
         '2.5.1' : 'c2a7b519e32197a120cdf47e0f194f81', \
+        '2.5.2' : 'bd2f18346c788eb54e1e52f4f6acf41a', \
         }
 
 # parse and process arguments
@@ -129,7 +130,10 @@ if os.path.isfile("Makefile.lammps.%s" % mode):
   print("Creating Makefile.lammps")
   plumedinc = os.path.join('liblink', 'plumed', 'src', 'lib', 'Plumed.inc.' + mode)
   lines1 = open(plumedinc, 'r').readlines()
-  lines2 = open("Makefile.lammps.%s" % mode, 'r').readlines()
+  if (platform.system() == 'Darwin' and os.path.isfile("Makefile.lammps.%s.macosx" % mode)):
+    lines2 = open("Makefile.lammps.%s.macosx" % mode, 'r').readlines()
+  else:
+    lines2 = open("Makefile.lammps.%s" % mode, 'r').readlines()
   fp = open("Makefile.lammps", 'w')
   fp.write("PLUMED_LIBDIR=" + os.path.join(homedir, "lib\n"))
   for line in lines1:
diff --git a/lib/plumed/Makefile.lammps.runtime.macosx b/lib/plumed/Makefile.lammps.runtime.macosx
new file mode 100644
index 0000000000..d0ae6e82a5
--- /dev/null
+++ b/lib/plumed/Makefile.lammps.runtime.macosx
@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+plumed_SYSINC = -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=$(PLUMED_LIBDIR)/libplumedKernel.dylib
+plumed_SYSLIB = $(PLUMED_LOAD) -rdynamic
+plumed_SYSPATH = 
diff --git a/lib/plumed/README b/lib/plumed/README
index fb8ef29ff3..0d5f52f6b2 100644
--- a/lib/plumed/README
+++ b/lib/plumed/README
@@ -1,7 +1,7 @@
 This directory contains links to the PLUMED library which is required
 to use the PLUMED package and its fix plumed command in a
-LAMMPS input script.  PLUMED should only be downloaded into this directory if 
-you wish to statically link the library.  If you wish to link PLUMED as 
+LAMMPS input script.  PLUMED should only be downloaded into this directory if
+you wish to statically link the library.  If you wish to link PLUMED as
 a dynamic library (as we recommend) then you can compile and build PLUMED
 separately to LAMMPS.  To use PLUMED in conjuction with LAMMPS you then simply
 need to ensure that the PLUMED library is in your path at runtime.
@@ -18,15 +18,15 @@ below.
 
 Instructions:
 
-1.  Download PLUMED either as a tarball from 
+1.  Download PLUMED either as a tarball from
     http://www.plumed.org/get-it
-    or clone it using git clone https://github.com/plumed/plumed2.git. 
+    or clone it using git clone https://github.com/plumed/plumed2.git.
     If you download the tarball
     unpack it in unpack it in this /lib/plumed directory.
     Similarly if you clone it clone it to the /lib/plumed
     directory.
 
-2.  Compile PLUMED from within its home directory.  In the 
+2.  Compile PLUMED from within its home directory.  In the
     simplest cases this be done by issuing the commands
     % ./configure
     % make
@@ -34,14 +34,14 @@ Instructions:
     http://plumed.github.io/doc-master/user-doc/html/_installation.html
 
 3.  There is no need to install PLUMED if you only wish
-    to use it from LAMMPS.  You should thus only run 
+    to use it from LAMMPS.  You should thus only run
     make install if you want to use PLUMED as a stand-alone
-    code or from some other code.  To install it you can 
+    code or from some other code.  To install it you can
     run the following commands:
     a) install under the default /usr/local
        % sudo make install
     b) install under a user-writeable location by first
-         changing the PREFIX variable when running the 
+         changing the PREFIX variable when running the
          configure command file, then
        % make install
 
diff --git a/lib/poems/system.h b/lib/poems/system.h
index 1b59395de7..573044ce33 100644
--- a/lib/poems/system.h
+++ b/lib/poems/system.h
@@ -15,7 +15,6 @@
  *      CONTACT:        anderk5@rpi.edu                                    *
  *_________________________________________________________________________*/
 
- 
 #ifndef SYSTEM_H
 #define SYSTEM_H
 
@@ -31,7 +30,6 @@
 #include "workspace.h"
 #include "matrixfun.h"
 #include "onsolver.h"
-#include "system.h"
 #include "inertialframe.h"
 #include "rigidbody.h"
 #include "revolutejoint.h"
diff --git a/lib/vtk/Makefile.lammps.ubuntu18.04_vtk7 b/lib/vtk/Makefile.lammps.ubuntu18.04_vtk7
new file mode 100644
index 0000000000..c833a5f67c
--- /dev/null
+++ b/lib/vtk/Makefile.lammps.ubuntu18.04_vtk7
@@ -0,0 +1,12 @@
+# Settings that the LAMMPS build will import when this package library is used
+#
+# Ubuntu 18.04 installation of VTK7 library:
+# ------------------------------------------
+#
+# Execute the following installation command:
+#
+# $ sudo apt-get install libvtk7-dev
+#
+vtk_SYSINC = -I/usr/include/vtk7.1
+vtk_SYSLIB = -lvtkCommonCore-7.1 -lvtkIOCore-7.1 -lvtkIOXML-7.1 -lvtkIOLegacy-7.1 -lvtkCommonDataModel-7.1 -lvtkIOParallelXML-7.1
+vtk_SYSPATH = -L/usr/lib/x86_64-linux-gnu
diff --git a/python/lammps.py b/python/lammps.py
index 9b3790f2db..36cf2d2fdd 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -219,6 +219,12 @@ class lammps(object):
     self.c_imageint = get_ctypes_int(self.extract_setting("imageint"))
     self._installed_packages = None
 
+    # add way to insert Python callback for fix external
+    self.callback = {}
+    self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, c_void_p, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
+    self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, c_void_p]
+    self.lib.lammps_set_fix_external_callback.restype = None
+
   # shut-down LAMMPS instance
 
   def __del__(self):
@@ -602,6 +608,42 @@ class lammps(object):
         self._installed_packages.append(sb.value.decode())
     return self._installed_packages
 
+  def set_fix_external_callback(self, fix_name, callback, caller=None):
+    import numpy as np
+    def _ctype_to_numpy_int(ctype_int):
+          if ctype_int == c_int32:
+            return np.int32
+          elif ctype_int == c_int64:
+            return np.int64
+          return np.intc
+
+    def callback_wrapper(caller_ptr, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr):
+      if cast(caller_ptr,POINTER(py_object)).contents:
+        pyCallerObj = cast(caller_ptr,POINTER(py_object)).contents.value
+      else:
+        pyCallerObj = None
+
+      tptr = cast(tag_ptr, POINTER(self.c_tagint * nlocal))
+      tag = np.frombuffer(tptr.contents, dtype=_ctype_to_numpy_int(self.c_tagint))
+      tag.shape = (nlocal)
+
+      xptr = cast(x_ptr[0], POINTER(c_double * nlocal * 3))
+      x = np.frombuffer(xptr.contents)
+      x.shape = (nlocal, 3)
+
+      fptr = cast(fext_ptr[0], POINTER(c_double * nlocal * 3))
+      f = np.frombuffer(fptr.contents)
+      f.shape = (nlocal, 3)
+
+      callback(pyCallerObj, ntimestep, nlocal, tag, x, f)
+
+    cFunc   = self.FIX_EXTERNAL_CALLBACK_FUNC(callback_wrapper)
+    cCaller = cast(pointer(py_object(caller)), c_void_p)
+
+    self.callback[fix_name] = { 'function': cFunc, 'caller': caller }
+
+    self.lib.lammps_set_fix_external_callback(self.lmp, fix_name.encode(), cFunc, cCaller)
+
 # -------------------------------------------------------------------------
 # -------------------------------------------------------------------------
 # -------------------------------------------------------------------------
@@ -872,8 +914,8 @@ class PyLammps(object):
     output = self.__getattr__('run')(*args, **kwargs)
 
     if(lammps.has_mpi4py):
-      output = self.lmp.comm.bcast(output, root=0) 
-    
+      output = self.lmp.comm.bcast(output, root=0)
+
     self.runs += get_thermo_data(output)
     return output
 
diff --git a/src/.gitignore b/src/.gitignore
index c79c958e6d..2d79018b28 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -801,6 +801,8 @@
 /pair_comb3.h
 /pair_colloid.cpp
 /pair_colloid.h
+/pair_cosine_squared.cpp
+/pair_cosine_squared.h
 /pair_coul_diel.cpp
 /pair_coul_diel.h
 /pair_coul_long.cpp
diff --git a/src/ASPHERE/compute_erotate_asphere.cpp b/src/ASPHERE/compute_erotate_asphere.cpp
index afec2a9b28..3cf23b87eb 100644
--- a/src/ASPHERE/compute_erotate_asphere.cpp
+++ b/src/ASPHERE/compute_erotate_asphere.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "compute_erotate_asphere.h"
+#include <mpi.h>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
@@ -20,7 +20,6 @@
 #include "atom_vec_tri.h"
 #include "update.h"
 #include "force.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp
index 651c228e41..4350678bbd 100644
--- a/src/ASPHERE/compute_temp_asphere.cpp
+++ b/src/ASPHERE/compute_temp_asphere.cpp
@@ -15,9 +15,9 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "compute_temp_asphere.h"
 #include <mpi.h>
 #include <cstring>
-#include "compute_temp_asphere.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
@@ -26,7 +26,6 @@
 #include "domain.h"
 #include "modify.h"
 #include "group.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/ASPHERE/fix_nh_asphere.cpp b/src/ASPHERE/fix_nh_asphere.cpp
index 828c064a52..2f8f11978e 100644
--- a/src/ASPHERE/fix_nh_asphere.cpp
+++ b/src/ASPHERE/fix_nh_asphere.cpp
@@ -15,15 +15,10 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
-#include "math_extra.h"
 #include "fix_nh_asphere.h"
+#include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "group.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp
index 5f201a8463..70880701ca 100644
--- a/src/ASPHERE/fix_nph_asphere.cpp
+++ b/src/ASPHERE/fix_nph_asphere.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nph_asphere.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp
index 5d52891169..26d4fff81d 100644
--- a/src/ASPHERE/fix_npt_asphere.cpp
+++ b/src/ASPHERE/fix_npt_asphere.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_npt_asphere.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp
index 61e3c35293..93ccf008f4 100644
--- a/src/ASPHERE/fix_nve_asphere.cpp
+++ b/src/ASPHERE/fix_nve_asphere.cpp
@@ -15,16 +15,10 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_asphere.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "force.h"
-#include "update.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp
index 9cc430592a..3a7d7e86e9 100644
--- a/src/ASPHERE/fix_nve_asphere_noforce.cpp
+++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp
@@ -11,16 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
 #include "fix_nve_asphere_noforce.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "group.h"
-#include "update.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp
index 51a502df89..5e17cb355f 100644
--- a/src/ASPHERE/fix_nve_line.cpp
+++ b/src/ASPHERE/fix_nve_line.cpp
@@ -11,9 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_line.h"
 #include "atom.h"
 #include "atom_vec_line.h"
diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp
index fb9bf64c58..797fea1c5b 100644
--- a/src/ASPHERE/fix_nve_tri.cpp
+++ b/src/ASPHERE/fix_nve_tri.cpp
@@ -11,9 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_tri.h"
 #include "math_extra.h"
 #include "atom.h"
diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp
index 5ef91923eb..597fb03514 100644
--- a/src/ASPHERE/fix_nvt_asphere.cpp
+++ b/src/ASPHERE/fix_nvt_asphere.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nvt_asphere.h"
+#include <cstring>
 #include "group.h"
 #include "modify.h"
 #include "error.h"
diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp
index 3d4ed3f183..93b164c503 100644
--- a/src/ASPHERE/pair_gayberne.cpp
+++ b/src/ASPHERE/pair_gayberne.cpp
@@ -15,11 +15,9 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_gayberne.h"
+#include <mpi.h>
+#include <cmath>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
@@ -27,7 +25,6 @@
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "integrate.h"
 #include "citeme.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp
index 4873b44dc4..fdeb09aac4 100644
--- a/src/ASPHERE/pair_line_lj.cpp
+++ b/src/ASPHERE/pair_line_lj.cpp
@@ -11,11 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_line_lj.h"
+#include <cmath>
 #include "atom.h"
 #include "atom_vec_line.h"
 #include "force.h"
diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp
index b100a5f184..f139564320 100644
--- a/src/ASPHERE/pair_resquared.cpp
+++ b/src/ASPHERE/pair_resquared.cpp
@@ -15,11 +15,9 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_resquared.h"
+#include <mpi.h>
+#include <cmath>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
@@ -27,7 +25,6 @@
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "integrate.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp
index cefd73f976..0984b0a30c 100644
--- a/src/ASPHERE/pair_tri_lj.cpp
+++ b/src/ASPHERE/pair_tri_lj.cpp
@@ -11,11 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_tri_lj.h"
+#include <cmath>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_tri.h"
diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp
index 10529ad3af..696ebcce7d 100644
--- a/src/BODY/body_nparticle.cpp
+++ b/src/BODY/body_nparticle.cpp
@@ -11,8 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "body_nparticle.h"
+#include <cstring>
+#include <cstdlib>
+#include "my_pool_chunk.h"
 #include "math_extra.h"
 #include "atom_vec_body.h"
 #include "atom.h"
@@ -44,6 +46,7 @@ BodyNparticle::BodyNparticle(LAMMPS *lmp, int narg, char **arg) :
 
   icp = new MyPoolChunk<int>(1,1);
   dcp = new MyPoolChunk<double>(3*nmin,3*nmax);
+  maxexchange = 1 + 3*nmax;        // icp max + dcp max
 
   memory->create(imflag,nmax,"body/nparticle:imflag");
   memory->create(imdata,nmax,4,"body/nparticle:imdata");
diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp
index d352c789d7..d60372781a 100644
--- a/src/BODY/body_rounded_polygon.cpp
+++ b/src/BODY/body_rounded_polygon.cpp
@@ -15,8 +15,10 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "body_rounded_polygon.h"
+#include <cmath>
+#include <cstring>
+#include "my_pool_chunk.h"
 #include "atom_vec_body.h"
 #include "atom.h"
 #include "force.h"
@@ -61,6 +63,7 @@ BodyRoundedPolygon::BodyRoundedPolygon(LAMMPS *lmp, int narg, char **arg) :
 
   icp = new MyPoolChunk<int>(1,1);
   dcp = new MyPoolChunk<double>(3*nmin+2*nmin+1+1,3*nmax+2*nmax+1+1);
+  maxexchange = 1 + 3*nmax+2*nmax+1+1;      // icp max + dcp max
 
   memory->create(imflag,nmax,"body/rounded/polygon:imflag");
   memory->create(imdata,nmax,7,"body/nparticle:imdata");
diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp
index 99a380a932..49ec6f1d78 100644
--- a/src/BODY/body_rounded_polyhedron.cpp
+++ b/src/BODY/body_rounded_polyhedron.cpp
@@ -15,12 +15,14 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "body_rounded_polyhedron.h"
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
+#include "my_pool_chunk.h"
 #include "atom_vec_body.h"
 #include "atom.h"
 #include "force.h"
-#include "domain.h"
 #include "math_extra.h"
 #include "memory.h"
 #include "error.h"
@@ -61,6 +63,7 @@ BodyRoundedPolyhedron::BodyRoundedPolyhedron(LAMMPS *lmp, int narg, char **arg)
   icp = new MyPoolChunk<int>(1,3);
   dcp = new MyPoolChunk<double>(3*nmin+2+1+1,
                                 3*nmax+2*nmax+MAX_FACE_SIZE*nmax+1+1);
+  maxexchange = 3 + 3*nmax+2*nmax+MAX_FACE_SIZE*nmax+1+1;  // icp max + dcp max
 
   memory->create(imflag,2*nmax,"body/rounded/polyhedron:imflag");
   memory->create(imdata,2*nmax,7,"body/polyhedron:imdata");
diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp
index 20f7d76708..c12502df42 100644
--- a/src/BODY/compute_body_local.cpp
+++ b/src/BODY/compute_body_local.cpp
@@ -11,16 +11,14 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
 #include "compute_body_local.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body.h"
 #include "update.h"
-#include "domain.h"
 #include "force.h"
-#include "bond.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp
index b560bdd11d..4cf9ac5009 100644
--- a/src/BODY/compute_temp_body.cpp
+++ b/src/BODY/compute_temp_body.cpp
@@ -16,9 +16,9 @@
    based on ComputeTempAsphere
 ------------------------------------------------------------------------- */
 
+#include "compute_temp_body.h"
 #include <mpi.h>
 #include <cstring>
-#include "compute_temp_body.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_body.h"
@@ -27,7 +27,6 @@
 #include "domain.h"
 #include "modify.h"
 #include "group.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/BODY/fix_nh_body.cpp b/src/BODY/fix_nh_body.cpp
index 9739842419..b9a0c81e15 100644
--- a/src/BODY/fix_nh_body.cpp
+++ b/src/BODY/fix_nh_body.cpp
@@ -16,15 +16,10 @@
    based on FixNHAsphere
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
-#include "math_extra.h"
 #include "fix_nh_body.h"
+#include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_body.h"
-#include "group.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp
index e647488bce..a65c951c96 100644
--- a/src/BODY/fix_nph_body.cpp
+++ b/src/BODY/fix_nph_body.cpp
@@ -15,8 +15,8 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nph_body.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp
index 3c30e9e4e9..7e8097486e 100644
--- a/src/BODY/fix_npt_body.cpp
+++ b/src/BODY/fix_npt_body.cpp
@@ -15,8 +15,8 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_npt_body.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/BODY/fix_nve_body.cpp b/src/BODY/fix_nve_body.cpp
index 0c74facf34..185e397540 100644
--- a/src/BODY/fix_nve_body.cpp
+++ b/src/BODY/fix_nve_body.cpp
@@ -11,16 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_body.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_body.h"
-#include "force.h"
-#include "update.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp
index 273b5e7fff..efb05143a1 100644
--- a/src/BODY/fix_nvt_body.cpp
+++ b/src/BODY/fix_nvt_body.cpp
@@ -15,8 +15,8 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nvt_body.h"
+#include <cstring>
 #include "group.h"
 #include "modify.h"
 #include "error.h"
diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp
index 221937461b..e51476de60 100644
--- a/src/BODY/fix_wall_body_polygon.cpp
+++ b/src/BODY/fix_wall_body_polygon.cpp
@@ -15,19 +15,15 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_wall_body_polygon.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body_rounded_polygon.h"
 #include "domain.h"
 #include "update.h"
 #include "force.h"
-#include "pair.h"
-#include "modify.h"
-#include "respa.h"
 #include "math_const.h"
 #include "math_extra.h"
 #include "memory.h"
diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp
index 24a9e51dad..42c62de436 100644
--- a/src/BODY/fix_wall_body_polyhedron.cpp
+++ b/src/BODY/fix_wall_body_polyhedron.cpp
@@ -15,19 +15,15 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_wall_body_polyhedron.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body_rounded_polyhedron.h"
 #include "domain.h"
 #include "update.h"
 #include "force.h"
-#include "pair.h"
-#include "modify.h"
-#include "respa.h"
 #include "math_const.h"
 #include "math_extra.h"
 #include "memory.h"
diff --git a/src/BODY/pair_body_nparticle.cpp b/src/BODY/pair_body_nparticle.cpp
index f2eb2aa520..bd7aba5455 100644
--- a/src/BODY/pair_body_nparticle.cpp
+++ b/src/BODY/pair_body_nparticle.cpp
@@ -11,11 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_body_nparticle.h"
+#include <cmath>
+#include <cstring>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_body.h"
diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp
index 69495ea57f..f5e18e9d89 100644
--- a/src/BODY/pair_body_rounded_polygon.cpp
+++ b/src/BODY/pair_body_rounded_polygon.cpp
@@ -18,11 +18,10 @@
          the contact history for friction forces.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_body_rounded_polygon.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_body.h"
diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp
index 60f6df3582..2df58d45cd 100644
--- a/src/BODY/pair_body_rounded_polyhedron.cpp
+++ b/src/BODY/pair_body_rounded_polyhedron.cpp
@@ -20,12 +20,10 @@
          the contact history for friction forces.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_body_rounded_polyhedron.h"
-#include "math_extra.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body_rounded_polyhedron.h"
@@ -41,7 +39,6 @@
 #include "math_const.h"
 
 using namespace LAMMPS_NS;
-using namespace MathExtra;
 using namespace MathConst;
 
 #define DELTA 10000
diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp
index d550767e5e..99e1b39c9d 100644
--- a/src/CLASS2/angle_class2.cpp
+++ b/src/CLASS2/angle_class2.cpp
@@ -15,10 +15,10 @@
    Contributing author: Eric Simon (Cray)
 ------------------------------------------------------------------------- */
 
+#include "angle_class2.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "angle_class2.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/CLASS2/angle_class2.h b/src/CLASS2/angle_class2.h
index 8444ada057..cc155747ac 100644
--- a/src/CLASS2/angle_class2.h
+++ b/src/CLASS2/angle_class2.h
@@ -20,7 +20,6 @@ AngleStyle(class2,AngleClass2)
 #ifndef LMP_ANGLE_CLASS2_H
 #define LMP_ANGLE_CLASS2_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp
index 26c4e63a4d..cfc1a93bde 100644
--- a/src/CLASS2/bond_class2.cpp
+++ b/src/CLASS2/bond_class2.cpp
@@ -15,12 +15,11 @@
    Contributing author: Eric Simon (Cray)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "bond_class2.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/CLASS2/bond_class2.h b/src/CLASS2/bond_class2.h
index 89d930b548..f0fcc6825e 100644
--- a/src/CLASS2/bond_class2.h
+++ b/src/CLASS2/bond_class2.h
@@ -20,7 +20,6 @@ BondStyle(class2,BondClass2)
 #ifndef LMP_BOND_CLASS2_H
 #define LMP_BOND_CLASS2_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp
index c471b1f353..725228666e 100644
--- a/src/CLASS2/dihedral_class2.cpp
+++ b/src/CLASS2/dihedral_class2.cpp
@@ -15,14 +15,13 @@
    Contributing author: Eric Simon (Cray)
 ------------------------------------------------------------------------- */
 
+#include "dihedral_class2.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "dihedral_class2.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "update.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "math_const.h"
diff --git a/src/CLASS2/dihedral_class2.h b/src/CLASS2/dihedral_class2.h
index a4ea9e4bd9..32cd289137 100644
--- a/src/CLASS2/dihedral_class2.h
+++ b/src/CLASS2/dihedral_class2.h
@@ -20,7 +20,6 @@ DihedralStyle(class2,DihedralClass2)
 #ifndef LMP_DIHEDRAL_CLASS2_H
 #define LMP_DIHEDRAL_CLASS2_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp
index ccb81aebd9..ca7ac95239 100644
--- a/src/CLASS2/improper_class2.cpp
+++ b/src/CLASS2/improper_class2.cpp
@@ -15,14 +15,13 @@
    Contributing author: Eric Simon (Cray)
 ------------------------------------------------------------------------- */
 
+#include "improper_class2.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "improper_class2.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "update.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "math_const.h"
diff --git a/src/CLASS2/improper_class2.h b/src/CLASS2/improper_class2.h
index 1cc3417731..cac805046a 100644
--- a/src/CLASS2/improper_class2.h
+++ b/src/CLASS2/improper_class2.h
@@ -20,7 +20,6 @@ ImproperStyle(class2,ImproperClass2)
 #ifndef LMP_IMPROPER_CLASS2_H
 #define LMP_IMPROPER_CLASS2_H
 
-#include <cstdio>
 #include "improper.h"
 
 namespace LAMMPS_NS {
diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp
index 60b988926a..a0088e52b7 100644
--- a/src/CLASS2/pair_lj_class2.cpp
+++ b/src/CLASS2/pair_lj_class2.cpp
@@ -9,11 +9,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_class2.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -21,7 +20,6 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "math_const.h"
 #include "memory.h"
diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp
index 8dc038b8fc..e999a3682e 100644
--- a/src/CLASS2/pair_lj_class2_coul_cut.cpp
+++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_class2_coul_cut.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp
index c92c7b78f1..b56c076996 100644
--- a/src/CLASS2/pair_lj_class2_coul_long.cpp
+++ b/src/CLASS2/pair_lj_class2_coul_long.cpp
@@ -11,17 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_class2_coul_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp
index 095d01eef3..58593a99b1 100644
--- a/src/COLLOID/fix_wall_colloid.cpp
+++ b/src/COLLOID/fix_wall_colloid.cpp
@@ -15,13 +15,11 @@
    Contributing authors: Jeremy Lechman (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
 #include "fix_wall_colloid.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "atom_vec.h"
-#include "update.h"
-#include "respa.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp
index aefa96b1fb..71a5f8c056 100644
--- a/src/COLLOID/pair_brownian.cpp
+++ b/src/COLLOID/pair_brownian.cpp
@@ -15,23 +15,19 @@
    Contributing authors: Amit Kumar and Michael Bybee (UIUC)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_brownian.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "domain.h"
 #include "update.h"
 #include "modify.h"
 #include "fix.h"
-#include "fix_deform.h"
 #include "fix_wall.h"
 #include "input.h"
 #include "variable.h"
diff --git a/src/COLLOID/pair_brownian_poly.cpp b/src/COLLOID/pair_brownian_poly.cpp
index 389ae084b7..c3eb4f28a5 100644
--- a/src/COLLOID/pair_brownian_poly.cpp
+++ b/src/COLLOID/pair_brownian_poly.cpp
@@ -16,14 +16,11 @@
                          Dave Heine (Corning), polydispersity
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_brownian_poly.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
@@ -32,14 +29,12 @@
 #include "update.h"
 #include "modify.h"
 #include "fix.h"
-#include "fix_deform.h"
 #include "fix_wall.h"
 #include "input.h"
 #include "variable.h"
 #include "random_mars.h"
 #include "math_const.h"
 #include "math_special.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp
index 04c35a7c00..ad25184181 100644
--- a/src/COLLOID/pair_colloid.cpp
+++ b/src/COLLOID/pair_colloid.cpp
@@ -15,15 +15,12 @@
    Contributing author: Pieter in 't Veld (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_colloid.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "math_special.h"
 #include "memory.h"
diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp
index 4e629bd442..4492de3cbb 100644
--- a/src/COLLOID/pair_lubricate.cpp
+++ b/src/COLLOID/pair_lubricate.cpp
@@ -16,18 +16,15 @@
                          Amit Kumar and Michael Bybee (UIUC)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lubricate.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "domain.h"
 #include "modify.h"
 #include "fix.h"
@@ -35,7 +32,6 @@
 #include "fix_wall.h"
 #include "input.h"
 #include "variable.h"
-#include "random_mars.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp
index 3ea3d4fe4a..4f7e3917e8 100644
--- a/src/COLLOID/pair_lubricateU.cpp
+++ b/src/COLLOID/pair_lubricateU.cpp
@@ -15,25 +15,20 @@
    Contributing authors: Amit Kumar and Michael Bybee (UIUC)
 ------------------------------------------------------------------------- */
 
+#include "pair_lubricateU.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
-#include "pair_lubricateU.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "domain.h"
 #include "update.h"
 #include "math_const.h"
 #include "modify.h"
 #include "fix.h"
-#include "fix_deform.h"
 #include "fix_wall.h"
 #include "input.h"
 #include "variable.h"
diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp
index 4fec95dcd8..0f16d94300 100644
--- a/src/COLLOID/pair_lubricateU_poly.cpp
+++ b/src/COLLOID/pair_lubricateU_poly.cpp
@@ -17,24 +17,19 @@
                          Dave Heine (Corning), polydispersity
 ------------------------------------------------------------------------- */
 
+#include "pair_lubricateU_poly.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
-#include "pair_lubricateU_poly.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "domain.h"
-#include "update.h"
 #include "modify.h"
 #include "fix.h"
-#include "fix_deform.h"
 #include "fix_wall.h"
 #include "input.h"
 #include "variable.h"
diff --git a/src/COLLOID/pair_lubricate_poly.cpp b/src/COLLOID/pair_lubricate_poly.cpp
index ffbe7fce3c..e347441cf4 100644
--- a/src/COLLOID/pair_lubricate_poly.cpp
+++ b/src/COLLOID/pair_lubricate_poly.cpp
@@ -17,13 +17,11 @@
                          Dave Heine (Corning), polydispersity
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lubricate_poly.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
@@ -33,8 +31,6 @@
 #include "modify.h"
 #include "fix.h"
 #include "fix_deform.h"
-#include "memory.h"
-#include "random_mars.h"
 #include "fix_wall.h"
 #include "input.h"
 #include "variable.h"
diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp
index ab7d088508..1866fa60b5 100644
--- a/src/COLLOID/pair_yukawa_colloid.cpp
+++ b/src/COLLOID/pair_yukawa_colloid.cpp
@@ -15,16 +15,13 @@
    Contributing authors: Randy Schunk (Sandia)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_yukawa_colloid.h"
+#include <cmath>
 #include "atom.h"
 #include "atom_vec.h"
 #include "force.h"
-#include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp
index 7be1a10fe2..c76b7afa17 100644
--- a/src/COMPRESS/dump_xyz_gz.cpp
+++ b/src/COMPRESS/dump_xyz_gz.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "dump_xyz_gz.h"
-#include "domain.h"
 #include "error.h"
 #include "update.h"
 
diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp
index dac0d60fce..0dc03e47f2 100644
--- a/src/CORESHELL/compute_temp_cs.cpp
+++ b/src/CORESHELL/compute_temp_cs.cpp
@@ -16,11 +16,9 @@
                         (hendrik.heenen at mytum.com)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
-#include <cstring>
-#include <cmath>
 #include "compute_temp_cs.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "domain.h"
@@ -28,7 +26,6 @@
 #include "force.h"
 #include "group.h"
 #include "modify.h"
-#include "fix.h"
 #include "fix_store.h"
 #include "comm.h"
 #include "memory.h"
diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.cpp b/src/CORESHELL/pair_born_coul_dsf_cs.cpp
index f4d7447ade..9440bca109 100644
--- a/src/CORESHELL/pair_born_coul_dsf_cs.cpp
+++ b/src/CORESHELL/pair_born_coul_dsf_cs.cpp
@@ -16,19 +16,13 @@
    References: Fennell and Gezelter, JCP 124, 234104 (2006)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_born_coul_dsf_cs.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "math_const.h"
-#include "memory.h"
-#include "error.h"
 #include "math_special.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/CORESHELL/pair_born_coul_long_cs.cpp b/src/CORESHELL/pair_born_coul_long_cs.cpp
index a19f8c34a8..b56389e180 100644
--- a/src/CORESHELL/pair_born_coul_long_cs.cpp
+++ b/src/CORESHELL/pair_born_coul_long_cs.cpp
@@ -15,23 +15,13 @@
    Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_born_coul_long_cs.h"
+#include <cmath>
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
-#include "kspace.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define EWALD_F   1.12837917
 #define EWALD_P   9.95473818e-1
diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp
index 7b52c28664..398c2ba1ee 100644
--- a/src/CORESHELL/pair_born_coul_wolf_cs.cpp
+++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp
@@ -12,24 +12,16 @@
 ------------------------------------------------------------------------- */
 
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_born_coul_wolf_cs.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "math_const.h"
-#include "math_special.h"
-#include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
-using namespace MathSpecial;
 
 #define EPSILON 1.0e-20
 
diff --git a/src/CORESHELL/pair_buck_coul_long_cs.cpp b/src/CORESHELL/pair_buck_coul_long_cs.cpp
index 8df91f39a3..1392ec1880 100644
--- a/src/CORESHELL/pair_buck_coul_long_cs.cpp
+++ b/src/CORESHELL/pair_buck_coul_long_cs.cpp
@@ -15,23 +15,13 @@
    Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_buck_coul_long_cs.h"
+#include <cmath>
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
-#include "kspace.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define EWALD_F   1.12837917
 #define EWALD_P   9.95473818e-1
diff --git a/src/CORESHELL/pair_coul_long_cs.cpp b/src/CORESHELL/pair_coul_long_cs.cpp
index c8c8387d6d..8280799389 100644
--- a/src/CORESHELL/pair_coul_long_cs.cpp
+++ b/src/CORESHELL/pair_coul_long_cs.cpp
@@ -15,22 +15,11 @@
    Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_long_cs.h"
+#include <cmath>
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
-#include "kspace.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
-#include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/CORESHELL/pair_coul_wolf_cs.cpp b/src/CORESHELL/pair_coul_wolf_cs.cpp
index 36e037bfc8..20b7339480 100644
--- a/src/CORESHELL/pair_coul_wolf_cs.cpp
+++ b/src/CORESHELL/pair_coul_wolf_cs.cpp
@@ -11,25 +11,16 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_wolf_cs.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "math_const.h"
-#include "math_special.h"
-#include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
-using namespace MathSpecial;
 
 #define EPSILON 1.0e-20
 
diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
index 56c75f0f5d..7ad544051a 100644
--- a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
+++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
@@ -15,27 +15,13 @@
    Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_coul_long_cs.h"
+#include <cmath>
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
-#include "kspace.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define EWALD_F   1.12837917
 #define EWALD_P   9.95473818e-1
diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp
index a6f454dc98..0b6a27888f 100644
--- a/src/DIPOLE/atom_vec_dipole.cpp
+++ b/src/DIPOLE/atom_vec_dipole.cpp
@@ -11,13 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "atom_vec_dipole.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "memory.h"
diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
index 18b78c55e0..14c511c100 100644
--- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
+++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_dipole_cut.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp
index 42446a3777..fe020ed2e6 100644
--- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp
+++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_dipole_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp
index fbdc47a15b..5e7819c2f4 100644
--- a/src/DIPOLE/pair_lj_long_dipole_long.cpp
+++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp
@@ -15,23 +15,19 @@
    Contributing author: Pieter J. in 't Veld and Stan Moore (Sandia)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_long_dipole_long.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "math_const.h"
 #include "math_vector.h"
-#include "pair_lj_long_dipole_long.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
-#include "integrate.h"
-#include "respa.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp
index f0558e6a02..d4397503dc 100644
--- a/src/GPU/fix_gpu.cpp
+++ b/src/GPU/fix_gpu.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_gpu.h"
 #include <cstring>
 #include <cstdlib>
-#include "fix_gpu.h"
 #include "atom.h"
 #include "force.h"
 #include "pair.h"
diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp
index 9f76975ef1..d4d36a5837 100644
--- a/src/GPU/pair_beck_gpu.cpp
+++ b/src/GPU/pair_beck_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_beck_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_beck_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp
index 291ad8ad1f..7314024d71 100644
--- a/src/GPU/pair_born_coul_long_cs_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (Northwestern)
 ------------------------------------------------------------------------- */
 
+#include "pair_born_coul_long_cs_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_born_coul_long_cs_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp
index eb204691c7..79c0d5f147 100644
--- a/src/GPU/pair_born_coul_long_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_born_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_born_coul_long_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
index 4877a442b5..5f74d3fc7c 100644
--- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
+++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing authors: Trung Dac Nguyen (Northwestern)
 ------------------------------------------------------------------------- */
 
+#include "pair_born_coul_wolf_cs_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_born_coul_wolf_cs_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp
index 851174988b..693c2abffb 100644
--- a/src/GPU/pair_born_coul_wolf_gpu.cpp
+++ b/src/GPU/pair_born_coul_wolf_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing authors: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_born_coul_wolf_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_born_coul_wolf_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp
index 253d2d7282..e9edc4f1c2 100644
--- a/src/GPU/pair_born_gpu.cpp
+++ b/src/GPU/pair_born_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_born_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_born_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp
index ed602f9cab..182673fb0d 100644
--- a/src/GPU/pair_buck_coul_cut_gpu.cpp
+++ b/src/GPU/pair_buck_coul_cut_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing authors: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_buck_coul_cut_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_buck_coul_cut_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp
index d6b9e53282..75e784fafa 100644
--- a/src/GPU/pair_buck_coul_long_gpu.cpp
+++ b/src/GPU/pair_buck_coul_long_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_buck_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_buck_coul_long_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp
index 8c85407e6e..1559c45b88 100644
--- a/src/GPU/pair_buck_gpu.cpp
+++ b/src/GPU/pair_buck_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_buck_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_buck_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp
index 0ee8708b5b..4db18dbc52 100644
--- a/src/GPU/pair_colloid_gpu.cpp
+++ b/src/GPU/pair_colloid_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_colloid_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_colloid_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp
index fb50c446b1..8a3eb12f8d 100644
--- a/src/GPU/pair_coul_cut_gpu.cpp
+++ b/src/GPU/pair_coul_cut_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen
 ------------------------------------------------------------------------- */
 
+#include "pair_coul_cut_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_coul_cut_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp
index ec771a9935..1fc07f8dac 100644
--- a/src/GPU/pair_coul_debye_gpu.cpp
+++ b/src/GPU/pair_coul_debye_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ndtrung@umich.edu)
 ------------------------------------------------------------------------- */
 
+#include "pair_coul_debye_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_coul_debye_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp
index 1753b8a91c..408be036dd 100644
--- a/src/GPU/pair_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_coul_dsf_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_coul_dsf_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_coul_dsf_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp
index 6ca00d6361..c70424e472 100644
--- a/src/GPU/pair_coul_long_cs_gpu.cpp
+++ b/src/GPU/pair_coul_long_cs_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Nguyen (Northwestern)
 ------------------------------------------------------------------------- */
 
+#include "pair_coul_long_cs_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_coul_long_cs_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp
index f75d10b6dd..9623c25f2f 100644
--- a/src/GPU/pair_coul_long_gpu.cpp
+++ b/src/GPU/pair_coul_long_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Axel Kohlmeyer (Temple)
 ------------------------------------------------------------------------- */
 
+#include "pair_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_coul_long_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp
index b1e45fbecd..5fcad6a350 100644
--- a/src/GPU/pair_dpd_gpu.cpp
+++ b/src/GPU/pair_dpd_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_dpd_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_dpd_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp
index 0693a27344..2d6798a12d 100644
--- a/src/GPU/pair_dpd_tstat_gpu.cpp
+++ b/src/GPU/pair_dpd_tstat_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_dpd_tstat_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_dpd_tstat_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp
index 9b3412d3d1..bc55c66676 100644
--- a/src/GPU/pair_eam_alloy_gpu.cpp
+++ b/src/GPU/pair_eam_alloy_gpu.cpp
@@ -15,10 +15,10 @@
    Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_eam_alloy_gpu.h"
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_eam_alloy_gpu.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp
index 11ef28af3e..ac379a9ce6 100644
--- a/src/GPU/pair_eam_fs_gpu.cpp
+++ b/src/GPU/pair_eam_fs_gpu.cpp
@@ -15,10 +15,10 @@
    Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_eam_fs_gpu.h"
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_eam_fs_gpu.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp
index 4788a72417..57106f48a4 100644
--- a/src/GPU/pair_eam_gpu.cpp
+++ b/src/GPU/pair_eam_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_eam_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_eam_gpu.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/GPU/pair_eam_gpu.h b/src/GPU/pair_eam_gpu.h
index 099529f3df..e4742a3bef 100644
--- a/src/GPU/pair_eam_gpu.h
+++ b/src/GPU/pair_eam_gpu.h
@@ -20,7 +20,6 @@ PairStyle(eam/gpu,PairEAMGPU)
 #ifndef LMP_PAIR_EAM_GPU_H
 #define LMP_PAIR_EAM_GPU_H
 
-#include <cstdio>
 #include "pair_eam.h"
 
 namespace LAMMPS_NS {
diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp
index c596a9d644..842b84acf2 100644
--- a/src/GPU/pair_gauss_gpu.cpp
+++ b/src/GPU/pair_gauss_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_gauss_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_gauss_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp
index 4ed2750e57..f00accda15 100644
--- a/src/GPU/pair_gayberne_gpu.cpp
+++ b/src/GPU/pair_gayberne_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_gayberne_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_gayberne_gpu.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp
index 5bc30c809d..16b6b835c0 100644
--- a/src/GPU/pair_lj96_cut_gpu.cpp
+++ b/src/GPU/pair_lj96_cut_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj96_cut_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj96_cut_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
index 134295c69f..bacbb400b1 100644
--- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_charmm_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_charmm_coul_long_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
index fdffb06a8d..e34dbb0f99 100644
--- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_class2_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_class2_coul_long_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp
index bbb9168169..68f27598f3 100644
--- a/src/GPU/pair_lj_class2_gpu.cpp
+++ b/src/GPU/pair_lj_class2_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_class2_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_class2_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp
index 95eee6ae8f..542de37840 100644
--- a/src/GPU/pair_lj_cubic_gpu.cpp
+++ b/src/GPU/pair_lj_cubic_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_cubic_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_cubic_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
index 69fefbcdea..cf3dd711dc 100644
--- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_cut_coul_cut_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_cut_coul_cut_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
index de86c58647..20354e732c 100644
--- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_cut_coul_debye_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_cut_coul_debye_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
index 87eac52749..ccaf86efa6 100644
--- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_cut_coul_dsf_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_cut_coul_dsf_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
index c854dab83d..36c72f1143 100644
--- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_cut_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_cut_coul_long_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
index f87dc0ec91..79ca90698a 100644
--- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_cut_coul_msm_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_cut_coul_msm_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
index d2c925d950..e2c8b8d686 100644
--- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_cut_dipole_cut_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_cut_dipole_cut_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
index 774ff2fae4..fb76376d34 100644
--- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (Northwestern)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_cut_dipole_long_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_cut_dipole_long_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp
index 6dde9689f7..809e5cf05e 100644
--- a/src/GPU/pair_lj_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_cut_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_cut_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp
index 31f4fd651c..a530f7ff9a 100644
--- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Nguyen (Northwestern)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_expand_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_expand_coul_long_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp
index a2e1cf54e3..86f8a76b52 100644
--- a/src/GPU/pair_lj_expand_gpu.cpp
+++ b/src/GPU/pair_lj_expand_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Inderaj Bains (NVIDIA), ibains@nvidia.com
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_expand_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_expand_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp
index e03f4b2e50..78f8b8b461 100644
--- a/src/GPU/pair_lj_gromacs_gpu.cpp
+++ b/src/GPU/pair_lj_gromacs_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_gromacs_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_gromacs_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
index f5029df5dc..24ff8a4f28 100644
--- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_sdk_coul_long_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_sdk_coul_long_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp
index 4797a34408..2621f49aeb 100644
--- a/src/GPU/pair_lj_sdk_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_sdk_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_sdk_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
index dd25a70eee..cf26cdf3b4 100644
--- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
+++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_sf_dipole_sf_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_sf_dipole_sf_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp
index 838d28033f..f3a384113f 100644
--- a/src/GPU/pair_mie_cut_gpu.cpp
+++ b/src/GPU/pair_mie_cut_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_mie_cut_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_mie_cut_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp
index 1f94643e3a..dcad227045 100644
--- a/src/GPU/pair_morse_gpu.cpp
+++ b/src/GPU/pair_morse_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_morse_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_morse_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp
index 5e90f788bf..b12a790c81 100644
--- a/src/GPU/pair_resquared_gpu.cpp
+++ b/src/GPU/pair_resquared_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_resquared_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_resquared_gpu.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp
index 42adb02553..0efcb20c8d 100644
--- a/src/GPU/pair_soft_gpu.cpp
+++ b/src/GPU/pair_soft_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_soft_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_soft_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp
index 0cc858e57d..8999cb6c47 100644
--- a/src/GPU/pair_sw_gpu.cpp
+++ b/src/GPU/pair_sw_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_sw_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_sw_gpu.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_request.h"
diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp
index a0b6562e5e..4432265874 100644
--- a/src/GPU/pair_table_gpu.cpp
+++ b/src/GPU/pair_table_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing authors: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_table_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_table_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp
index cd0c5e6693..e0dc021b57 100644
--- a/src/GPU/pair_tersoff_gpu.cpp
+++ b/src/GPU/pair_tersoff_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
+#include "pair_tersoff_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_tersoff_gpu.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_request.h"
diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp
index fd55ddc6e6..a17efb55e8 100644
--- a/src/GPU/pair_tersoff_mod_gpu.cpp
+++ b/src/GPU/pair_tersoff_mod_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
+#include "pair_tersoff_mod_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_tersoff_mod_gpu.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_request.h"
diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp
index d3828962e2..765d25f8e6 100644
--- a/src/GPU/pair_tersoff_zbl_gpu.cpp
+++ b/src/GPU/pair_tersoff_zbl_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
 ------------------------------------------------------------------------- */
 
+#include "pair_tersoff_zbl_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_tersoff_zbl_gpu.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_request.h"
diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp
index 31422b0f4d..97c2eebf24 100644
--- a/src/GPU/pair_ufm_gpu.cpp
+++ b/src/GPU/pair_ufm_gpu.cpp
@@ -17,11 +17,11 @@
             Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
  ------------------------------------------------------------------------- */
 
+#include "pair_ufm_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_ufm_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp
index b496359b8a..3b74e5685e 100644
--- a/src/GPU/pair_vashishta_gpu.cpp
+++ b/src/GPU/pair_vashishta_gpu.cpp
@@ -14,12 +14,12 @@
 /* ----------------------------------------------------------------------
    Contributing author: Anders Hafreager (UiO)
 ------------------------------------------------------------------------- */
-#include <limits>
+
+#include "pair_vashishta_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_vashishta_gpu.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_request.h"
diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp
index 3645f392a2..51c7e683db 100644
--- a/src/GPU/pair_yukawa_colloid_gpu.cpp
+++ b/src/GPU/pair_yukawa_colloid_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_yukawa_colloid_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_yukawa_colloid_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp
index 90317fea34..5dc13c7750 100644
--- a/src/GPU/pair_yukawa_gpu.cpp
+++ b/src/GPU/pair_yukawa_gpu.cpp
@@ -15,11 +15,11 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_yukawa_gpu.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_yukawa_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp
index 99471cbe90..5e24281145 100644
--- a/src/GPU/pair_zbl_gpu.cpp
+++ b/src/GPU/pair_zbl_gpu.cpp
@@ -15,12 +15,12 @@
    Contributing author: Trung Dac Nguyen (ORNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_zbl_gpu.h"
 #include "lmptype.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_zbl_gpu.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp
index 1bb1a39703..bbb270ff8e 100644
--- a/src/GPU/pppm_gpu.cpp
+++ b/src/GPU/pppm_gpu.cpp
@@ -15,12 +15,12 @@
    Contributing authors: Mike Brown (ORNL), Axel Kohlmeyer (Temple)
 ------------------------------------------------------------------------- */
 
+#include "pppm_gpu.h"
 #include <mpi.h>
 #include <cstring>
 #include <cstdio>
 #include <cstdlib>
 #include <cmath>
-#include "pppm_gpu.h"
 #include "atom.h"
 #include "comm.h"
 #include "gridcomm.h"
diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp
index 73c1c9fc11..1df5c9d0a8 100644
--- a/src/GRANULAR/fix_freeze.cpp
+++ b/src/GRANULAR/fix_freeze.cpp
@@ -11,12 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_freeze.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
-#include "comm.h"
 #include "respa.h"
 #include "error.h"
 
diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp
index 3ffca8db9d..b62b630be5 100644
--- a/src/GRANULAR/fix_pour.cpp
+++ b/src/GRANULAR/fix_pour.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_pour.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "force.h"
@@ -32,6 +32,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -180,11 +181,9 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
   // assume grav = -magnitude at this point, enforce in init()
 
   int ifix;
-  for (ifix = 0; ifix < modify->nfix; ifix++) {
-    if (strcmp(modify->fix[ifix]->style,"gravity") == 0) break;
-    if (strcmp(modify->fix[ifix]->style,"gravity/omp") == 0) break;
-    if (strstr(modify->fix[ifix]->style,"gravity/kk") != NULL) break;
-  }
+  for (ifix = 0; ifix < modify->nfix; ifix++)
+    if (utils::strmatch(modify->fix[ifix]->style,"^gravity")) break;
+
   if (ifix == modify->nfix)
     error->all(FLERR,"No fix gravity defined for fix pour");
   grav = - ((FixGravity *) modify->fix[ifix])->magnitude * force->ftm2v;
diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp
index 8513fc702b..a6e67e06ff 100644
--- a/src/GRANULAR/fix_wall_gran.cpp
+++ b/src/GRANULAR/fix_wall_gran.cpp
@@ -16,15 +16,13 @@
                          Dan Bolintineanu (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_wall_gran.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "update.h"
 #include "force.h"
-#include "pair.h"
 #include "modify.h"
 #include "respa.h"
 #include "math_const.h"
@@ -1149,11 +1147,11 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
   else{
     knfac = E; //Hooke
     a = sqrt(dR);
+    Fne = knfac*delta;
     if (normal_model != HOOKE) {
       Fne *= a;
       knfac *= a;
     }
-    Fne = knfac*delta;
     if (normal_model == DMT)
       Fne -= 4*MY_PI*normal_coeffs[3]*Reff;
   }
@@ -1294,10 +1292,12 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
   // rolling resistance
   //****************************************
 
-  if (roll_model != ROLL_NONE) {
+  if (roll_model != ROLL_NONE || twist_model != NONE) {
     relrot1 = omega[0];
     relrot2 = omega[1];
     relrot3 = omega[2];
+  }
+  if (roll_model != ROLL_NONE){
 
     // rolling velocity, see eq. 31 of Wang et al, Particuology v 23, p 49 (2015)
     // This is different from the Marshall papers,
diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp
index 72798bf7b7..95553b83b7 100644
--- a/src/GRANULAR/fix_wall_gran_region.cpp
+++ b/src/GRANULAR/fix_wall_gran_region.cpp
@@ -15,19 +15,12 @@
    Contributing authors: Dan Bolintineanu (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_wall_gran_region.h"
+#include <cstring>
 #include "region.h"
 #include "atom.h"
 #include "domain.h"
 #include "update.h"
-#include "force.h"
-#include "pair.h"
-#include "modify.h"
-#include "respa.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "comm.h"
@@ -35,7 +28,6 @@
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
-using namespace MathConst;
 
 // same as FixWallGran
 
diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp
index 728491c17a..4a362c0928 100644
--- a/src/GRANULAR/pair_gran_hertz_history.cpp
+++ b/src/GRANULAR/pair_gran_hertz_history.cpp
@@ -15,11 +15,9 @@
    Contributing authors: Leo Silbert (SNL), Gary Grest (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstdio>
-#include <cstring>
 #include "pair_gran_hertz_history.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp
index cfcc2743ba..d4be320554 100644
--- a/src/GRANULAR/pair_gran_hooke.cpp
+++ b/src/GRANULAR/pair_gran_hooke.cpp
@@ -15,10 +15,8 @@
    Contributing authors: Leo Silbert (SNL), Gary Grest (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "pair_gran_hooke.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "fix.h"
diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp
index 5a78b9d79a..771a5566df 100644
--- a/src/GRANULAR/pair_gran_hooke_history.cpp
+++ b/src/GRANULAR/pair_gran_hooke_history.cpp
@@ -15,14 +15,11 @@
    Contributing authors: Leo Silbert (SNL), Gary Grest (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_gran_hooke_history.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp
index 77b1981786..b87e64a456 100644
--- a/src/GRANULAR/pair_granular.cpp
+++ b/src/GRANULAR/pair_granular.cpp
@@ -16,14 +16,11 @@ See the README file in the top-level LAMMPS directory.
    Leo Silbert (SNL), Gary Grest (SNL)
 ----------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstdio>
-#include <cstring>
 #include "pair_granular.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/KIM/README b/src/KIM/README
index a69206596f..e61f47426f 100644
--- a/src/KIM/README
+++ b/src/KIM/README
@@ -1,29 +1,30 @@
-This package provides a pair_style kim command which is a wrapper on
-the Knowledge Base for Interatomic Models (KIM) repository of
-interatomic potentials, so that they can be used by LAMMPS scripts.
+This package provides the kim_init, kim_query, kim_interactions, and
+the pair_style kim command which are wrappers on the Knowledgebase of
+Interatomic Models (KIM) repository of interatomic potentials, so that
+they can be used by LAMMPS scripts.
 
 Information about the KIM project can be found at https://openkim.org.
-The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn) and
-James Sethna (Cornell U).  Ryan Elliott is the main developer for the
-KIM API and he also maintains the code that implements the pair_style
-kim command.
+The KIM project is lead by Ellad B. Tadmor and Ryan S. Elliott (UMN).
+Ryan Elliott is the main developer for the KIM API and he also
+maintains the code that implements these commands.
 
-Using this package requires the KIM library and its models
+Using this package requires the KIM-API library and its models
 (interatomic potentials) to be downloaded and installed on your
 system.  The library can be downloaded and built in lib/kim or
 elsewhere on your system, which must be done before bulding LAMMPS
 with this package.  Details of the download, build, and install
-process for KIM are given in the lib/kim/README file, and scripts will
-soon be provided to help automate the process.  Also see the LAMMPS
-manual for general information on building LAMMPS with external
+process for the KIM-API are given in the lib/kim/README file, and
+scripts are provided to help automate the process.  Also see the
+LAMMPS manual for general information on building LAMMPS with external
 libraries.  The settings in the Makefile.lammps file in lib/kim must
 be correct for LAMMPS to build correctly with this package installed.
 However, the default settings should be correct in most cases and the
 Makefile.lammps file usually will not need to be changed.
 
 Once you have successfully built LAMMPS with this package and the KIM
-library you can test it using an input file from the examples dir:
+library you can test it using an input files in the examples dir:
 
-./lmp_serial < lammps/examples/kim/in.kim.lj
+./lmp_serial -in lammps/examples/kim/in.kim.lj
 
-This pair_style was written by Ryan S. Elliott (U Minn).
+These commands were written by Ryan S. Elliott (UMN), Ellad B. Tadmor
+(UMN) and Axel Kohlmeyer (Temple U).
diff --git a/src/KIM/fix_store_kim.cpp b/src/KIM/fix_store_kim.cpp
new file mode 100644
index 0000000000..16d606d2ed
--- /dev/null
+++ b/src/KIM/fix_store_kim.cpp
@@ -0,0 +1,155 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors: Axel Kohlmeyer (Temple U),
+                         Ryan S. Elliott (UMN)
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   This program is free software; you can redistribute it and/or modify it
+   under the terms of the GNU General Public License as published by the Free
+   Software Foundation; either version 2 of the License, or (at your option)
+   any later version.
+
+   This program is distributed in the hope that it will be useful, but WITHOUT
+   ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+   FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+   more details.
+
+   You should have received a copy of the GNU General Public License along with
+   this program; if not, see <https://www.gnu.org/licenses>.
+
+   Linking LAMMPS statically or dynamically with other modules is making a
+   combined work based on LAMMPS. Thus, the terms and conditions of the GNU
+   General Public License cover the whole combination.
+
+   In addition, as a special exception, the copyright holders of LAMMPS give
+   you permission to combine LAMMPS with free software programs or libraries
+   that are released under the GNU LGPL and with code included in the standard
+   release of the "kim-api" under the CDDL (or modified versions of such code,
+   with unchanged license). You may copy and distribute such a system following
+   the terms of the GNU GPL for LAMMPS and the licenses of the other code
+   concerned, provided that you include the source code of that other code
+   when and as the GNU GPL requires distribution of source code.
+
+   Note that people who make modified versions of LAMMPS are not obligated to
+   grant this special exception for their modified versions; it is their choice
+   whether to do so. The GNU General Public License gives permission to release
+   a modified version without this exception; this exception also makes it
+   possible to release a modified version which carries forward this exception.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Designed for use with the kim-api-2.0.2 (and newer) package
+------------------------------------------------------------------------- */
+
+#include "fix_store_kim.h"
+#include <cstring>
+extern "C" {
+#include "KIM_SimulatorModel.h"
+}
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ---------------------------------------------------------------------- */
+
+FixStoreKIM::FixStoreKIM(LAMMPS *lmp, int narg, char **arg)
+  : Fix(lmp, narg, arg), simulator_model(NULL), model_name(NULL),
+    model_units(NULL), user_units(NULL)
+{
+  if (narg != 3) error->all(FLERR,"Illegal fix STORE/KIM command");
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixStoreKIM::~FixStoreKIM()
+{
+  // free associated storage
+
+  if (simulator_model) {
+    KIM_SimulatorModel *sm = (KIM_SimulatorModel *)simulator_model;
+    KIM_SimulatorModel_Destroy(&sm);
+    simulator_model = NULL;
+  }
+
+  if (model_name) {
+    char *mn = (char *)model_name;
+    delete[] mn;
+    model_name = NULL;
+  }
+
+  if (model_units) {
+    char *mu = (char *)model_units;
+    delete[] mu;
+    model_units = NULL;
+  }
+  if (user_units) {
+    char *uu = (char *)user_units;
+    delete[] uu;
+    user_units = NULL;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixStoreKIM::setmask()
+{
+  int mask = 0;
+  return mask;
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+void FixStoreKIM::setptr(const char *name, void *ptr)
+{
+  if (strcmp(name,"simulator_model") == 0) {
+    if (simulator_model) {
+      KIM_SimulatorModel *sm = (KIM_SimulatorModel *)simulator_model;
+      KIM_SimulatorModel_Destroy(&sm);
+    }
+    simulator_model = ptr;
+  } else if (strcmp(name,"model_name") == 0) {
+    if (model_name) {
+      char *mn = (char *)model_name;
+      delete[] mn;
+    }
+    model_name = ptr;
+  } else if (strcmp(name,"model_units") == 0) {
+    if (model_units) {
+      char *mu = (char *)model_units;
+      delete[] mu;
+    }
+    model_units = ptr;
+  } else if (strcmp(name,"user_units") == 0) {
+    if (user_units) {
+      char *uu = (char *)user_units;
+      delete[] uu;
+    }
+    user_units = ptr;
+  } else error->all(FLERR,"Unknown property in fix STORE/KIM");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *FixStoreKIM::getptr(const char *name)
+{
+  if (strcmp(name,"simulator_model") == 0) return simulator_model;
+  else if (strcmp(name,"model_name") == 0) return model_name;
+  else if (strcmp(name,"model_units") == 0) return model_units;
+  else if (strcmp(name,"user_units") == 0) return user_units;
+  else return NULL;
+}
diff --git a/src/KIM/fix_store_kim.h b/src/KIM/fix_store_kim.h
new file mode 100644
index 0000000000..6baf480993
--- /dev/null
+++ b/src/KIM/fix_store_kim.h
@@ -0,0 +1,99 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors: Axel Kohlmeyer (Temple U),
+                         Ryan S. Elliott (UMN)
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   This program is free software; you can redistribute it and/or modify it
+   under the terms of the GNU General Public License as published by the Free
+   Software Foundation; either version 2 of the License, or (at your option)
+   any later version.
+
+   This program is distributed in the hope that it will be useful, but WITHOUT
+   ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+   FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+   more details.
+
+   You should have received a copy of the GNU General Public License along with
+   this program; if not, see <https://www.gnu.org/licenses>.
+
+   Linking LAMMPS statically or dynamically with other modules is making a
+   combined work based on LAMMPS. Thus, the terms and conditions of the GNU
+   General Public License cover the whole combination.
+
+   In addition, as a special exception, the copyright holders of LAMMPS give
+   you permission to combine LAMMPS with free software programs or libraries
+   that are released under the GNU LGPL and with code included in the standard
+   release of the "kim-api" under the CDDL (or modified versions of such code,
+   with unchanged license). You may copy and distribute such a system following
+   the terms of the GNU GPL for LAMMPS and the licenses of the other code
+   concerned, provided that you include the source code of that other code
+   when and as the GNU GPL requires distribution of source code.
+
+   Note that people who make modified versions of LAMMPS are not obligated to
+   grant this special exception for their modified versions; it is their choice
+   whether to do so. The GNU General Public License gives permission to release
+   a modified version without this exception; this exception also makes it
+   possible to release a modified version which carries forward this exception.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Designed for use with the kim-api-2.0.2 (and newer) package
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(STORE/KIM,FixStoreKIM)
+
+#else
+
+#ifndef LMP_FIX_STORE_KIM_H
+#define LMP_FIX_STORE_KIM_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixStoreKIM : public Fix {
+ public:
+  FixStoreKIM(class LAMMPS *, int, char **);
+  ~FixStoreKIM();
+  int setmask();
+
+  void  setptr(const char *, void *);
+  void *getptr(const char *);
+
+ private:
+  void *simulator_model;        // pointer to KIM simulator model class
+  void *model_name;             // string of KIM model name
+  void *model_units;            // string of unit conversion origin or NULL
+  void *user_units;             // string of unit conversion target or NULL
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+*/
diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp
new file mode 100644
index 0000000000..a4272caa01
--- /dev/null
+++ b/src/KIM/kim_init.cpp
@@ -0,0 +1,508 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors: Axel Kohlmeyer (Temple U),
+                         Ryan S. Elliott (UMN)
+                         Ellad B. Tadmor (UMN)
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   This program is free software; you can redistribute it and/or modify it
+   under the terms of the GNU General Public License as published by the Free
+   Software Foundation; either version 2 of the License, or (at your option)
+   any later version.
+
+   This program is distributed in the hope that it will be useful, but WITHOUT
+   ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+   FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+   more details.
+
+   You should have received a copy of the GNU General Public License along with
+   this program; if not, see <https://www.gnu.org/licenses>.
+
+   Linking LAMMPS statically or dynamically with other modules is making a
+   combined work based on LAMMPS. Thus, the terms and conditions of the GNU
+   General Public License cover the whole combination.
+
+   In addition, as a special exception, the copyright holders of LAMMPS give
+   you permission to combine LAMMPS with free software programs or libraries
+   that are released under the GNU LGPL and with code included in the standard
+   release of the "kim-api" under the CDDL (or modified versions of such code,
+   with unchanged license). You may copy and distribute such a system following
+   the terms of the GNU GPL for LAMMPS and the licenses of the other code
+   concerned, provided that you include the source code of that other code
+   when and as the GNU GPL requires distribution of source code.
+
+   Note that people who make modified versions of LAMMPS are not obligated to
+   grant this special exception for their modified versions; it is their choice
+   whether to do so. The GNU General Public License gives permission to release
+   a modified version without this exception; this exception also makes it
+   possible to release a modified version which carries forward this exception.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Designed for use with the kim-api-2.1.0 (and newer) package
+------------------------------------------------------------------------- */
+
+#include "kim_init.h"
+#include <cstring>
+#include <string>
+#include <sstream>
+#include <iomanip>
+#include "error.h"
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "modify.h"
+#include "update.h"
+#include "universe.h"
+#include "input.h"
+#include "variable.h"
+#include "citeme.h"
+#include "fix_store_kim.h"
+#include "kim_units.h"
+
+extern "C" {
+#include "KIM_SimulatorHeaders.h"
+}
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+void KimInit::command(int narg, char **arg)
+{
+  if ((narg < 2) || (narg > 3)) error->all(FLERR,"Illegal kim_init command");
+
+  if (domain->box_exist)
+    error->all(FLERR,"Must use 'kim_init' command before "
+                     "simulation box is defined");
+  char *model_name = new char[strlen(arg[0])+1];
+  strcpy(model_name,arg[0]);
+  char *user_units = new char[strlen(arg[1])+1];
+  strcpy(user_units,arg[1]);
+  if (narg == 3) {
+    if (strcmp(arg[2],"unit_conversion_mode")==0) unit_conversion_mode = true;
+    else { error->all(FLERR,"Illegal kim_init command"); }
+  } else unit_conversion_mode = false;
+
+  char *model_units;
+  determine_model_type_and_units(model_name, user_units, &model_units);
+
+  write_log_cite(model_name);
+
+  do_init(model_name, user_units, model_units);
+}
+
+
+/* ---------------------------------------------------------------------- */
+namespace {
+void get_kim_unit_names(
+    char const * const system,
+    KIM_LengthUnit & lengthUnit,
+    KIM_EnergyUnit & energyUnit,
+    KIM_ChargeUnit & chargeUnit,
+    KIM_TemperatureUnit & temperatureUnit,
+    KIM_TimeUnit & timeUnit,
+    Error * error)
+{
+  if ((strcmp(system,"real")==0)) {
+    lengthUnit = KIM_LENGTH_UNIT_A;
+    energyUnit = KIM_ENERGY_UNIT_kcal_mol;
+    chargeUnit = KIM_CHARGE_UNIT_e;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_fs;
+  } else if ((strcmp(system,"metal")==0)) {
+    lengthUnit = KIM_LENGTH_UNIT_A;
+    energyUnit = KIM_ENERGY_UNIT_eV;
+    chargeUnit = KIM_CHARGE_UNIT_e;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_ps;
+  } else if ((strcmp(system,"si")==0)) {
+    lengthUnit = KIM_LENGTH_UNIT_m;
+    energyUnit = KIM_ENERGY_UNIT_J;
+    chargeUnit = KIM_CHARGE_UNIT_C;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_s;
+  } else if ((strcmp(system,"cgs")==0)) {
+    lengthUnit = KIM_LENGTH_UNIT_cm;
+    energyUnit = KIM_ENERGY_UNIT_erg;
+    chargeUnit = KIM_CHARGE_UNIT_statC;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_s;
+  } else if ((strcmp(system,"electron")==0)) {
+    lengthUnit = KIM_LENGTH_UNIT_Bohr;
+    energyUnit = KIM_ENERGY_UNIT_Hartree;
+    chargeUnit = KIM_CHARGE_UNIT_e;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_fs;
+  } else if ((strcmp(system,"lj")==0)) {
+    error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models");
+  } else {
+    error->all(FLERR,"Unknown unit_style");
+  }
+}
+}  // namespace
+void KimInit::determine_model_type_and_units(char * model_name,
+                                             char * user_units,
+                                             char ** model_units)
+{
+  KIM_LengthUnit lengthUnit;
+  KIM_EnergyUnit energyUnit;
+  KIM_ChargeUnit chargeUnit;
+  KIM_TemperatureUnit temperatureUnit;
+  KIM_TimeUnit timeUnit;
+  int units_accepted;
+  KIM_Collections * kim_Coll;
+  KIM_CollectionItemType itemType;
+
+  int kim_error = KIM_Collections_Create(&kim_Coll);
+  if (kim_error) {
+    error->all(FLERR,"Unable to access KIM Collections to find Model.");
+  }
+
+  kim_error = KIM_Collections_GetItemType(kim_Coll, model_name, &itemType);
+  if (kim_error) {
+    error->all(FLERR,"KIM Model name not found.");
+  }
+  KIM_Collections_Destroy(&kim_Coll);
+
+  if (KIM_CollectionItemType_Equal(itemType,
+                                   KIM_COLLECTION_ITEM_TYPE_portableModel))
+  {
+    get_kim_unit_names(user_units, lengthUnit, energyUnit,
+                       chargeUnit, temperatureUnit, timeUnit, error);
+    KIM_Model * kim_MO;
+    int kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased,
+                                     lengthUnit,
+                                     energyUnit,
+                                     chargeUnit,
+                                     temperatureUnit,
+                                     timeUnit,
+                                     model_name,
+                                     &units_accepted,
+                                     &kim_MO);
+
+    if (kim_error)
+      error->all(FLERR,"Unable to load KIM Simulator Model.");
+
+    model_type = MO;
+    KIM_Model_Destroy(&kim_MO);
+
+    if (units_accepted) {
+      *model_units = new char[strlen(user_units)+1];
+      strcpy(*model_units,user_units);
+      return;
+    } else if (unit_conversion_mode) {
+      int const num_systems = 5;
+      char const * const systems[num_systems]
+          = {"metal", "real", "si", "cgs", "electron"};
+      for (int i=0; i < num_systems; ++i) {
+        get_kim_unit_names(systems[i], lengthUnit, energyUnit,
+                           chargeUnit, temperatureUnit, timeUnit, error);
+        kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased,
+                                     lengthUnit,
+                                     energyUnit,
+                                     chargeUnit,
+                                     temperatureUnit,
+                                     timeUnit,
+                                     model_name,
+                                     &units_accepted,
+                                     &kim_MO);
+        KIM_Model_Destroy(&kim_MO);
+        if (units_accepted) {
+          *model_units = new char[strlen(systems[i])+1];
+          strcpy(*model_units,systems[i]);
+          return;
+        }
+      } error->all(FLERR,"KIM Model does not support any lammps unit system");
+    } else {
+      error->all(FLERR,"KIM Model does not support the requested unit system");
+    }
+  }
+  else if (KIM_CollectionItemType_Equal(
+               itemType, KIM_COLLECTION_ITEM_TYPE_simulatorModel)) {
+    KIM_SimulatorModel * kim_SM;
+    kim_error = KIM_SimulatorModel_Create(model_name, &kim_SM);
+    if (kim_error)
+      error->all(FLERR,"Unable to load KIM Simulator Model.");
+    model_type = SM;
+
+    int sim_fields;
+    int sim_lines;
+    char const * sim_field;
+    char const * sim_value;
+    KIM_SimulatorModel_GetNumberOfSimulatorFields(kim_SM, &sim_fields);
+    KIM_SimulatorModel_CloseTemplateMap(kim_SM);
+    for (int i=0; i < sim_fields; ++i) {
+      KIM_SimulatorModel_GetSimulatorFieldMetadata(
+          kim_SM,i,&sim_lines,&sim_field);
+
+      if (0 == strcmp(sim_field,"units")) {
+        KIM_SimulatorModel_GetSimulatorFieldLine(kim_SM,i,0,&sim_value);
+        int len=strlen(sim_value)+1;
+        *model_units = new char[len]; strcpy(*model_units,sim_value);
+        break;
+      }
+    }
+    KIM_SimulatorModel_Destroy(&kim_SM);
+
+    if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) {
+      std::string mesg("Incompatible units for KIM Simulator Model, "
+                       "required units = ");
+      mesg += *model_units;
+      error->all(FLERR,mesg.c_str());
+    }
+  }
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+void KimInit::do_init(char *model_name, char *user_units, char *model_units)
+{
+  // create storage proxy fix. delete existing fix, if needed.
+
+  int ifix = modify->find_fix("KIM_MODEL_STORE");
+  if (ifix >= 0) modify->delete_fix(ifix);
+  char *fixarg[3];
+  fixarg[0] = (char *)"KIM_MODEL_STORE";
+  fixarg[1] = (char *)"all";
+  fixarg[2] = (char *)"STORE/KIM";
+  modify->add_fix(3,fixarg);
+  ifix = modify->find_fix("KIM_MODEL_STORE");
+
+  FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix];
+  fix_store->setptr("model_name", (void *) model_name);
+  fix_store->setptr("user_units", (void *) user_units);
+  fix_store->setptr("model_units", (void *) model_units);
+
+  // Begin output to log file
+  kim_init_log_delimiter("begin");
+
+  int kimerror;
+  KIM_SimulatorModel * simulatorModel;
+  if (model_type == SM)
+  {
+    kimerror = KIM_SimulatorModel_Create(model_name,&simulatorModel);
+
+    char const *sim_name, *sim_version;
+    KIM_SimulatorModel_GetSimulatorNameAndVersion(
+        simulatorModel,&sim_name, &sim_version);
+
+    if (0 != strcmp(sim_name,"LAMMPS"))
+      error->all(FLERR,"Incompatible KIM Simulator Model");
+
+    if (comm->me == 0) {
+      std::string mesg("# Using KIM Simulator Model : ");
+      mesg += model_name;
+      mesg += "\n";
+      mesg += "# For Simulator             : ";
+      mesg += std::string(sim_name) + " " + sim_version + "\n";
+      mesg += "# Running on                : LAMMPS ";
+      mesg += universe->version;
+      mesg += "\n";
+      mesg += "#\n";
+
+      if (screen) fputs(mesg.c_str(),screen);
+      if (logfile) fputs(mesg.c_str(),logfile);
+    }
+
+    fix_store->setptr("simulator_model", (void *) simulatorModel);
+
+    // need to call this to have access to (some) simulator model init data.
+
+    KIM_SimulatorModel_CloseTemplateMap(simulatorModel);
+  }
+
+  // Define unit conversion factor variables and print to log
+  if (unit_conversion_mode) do_variables(user_units, model_units);
+
+  // set units
+
+  std::string cmd("units ");
+  cmd += model_units;
+  input->one(cmd.c_str());
+
+  if (model_type == SM) {
+    int sim_fields, sim_lines;
+    char const *sim_field, *sim_value;
+    KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields);
+
+    // init model
+
+    for (int i=0; i < sim_fields; ++i) {
+      KIM_SimulatorModel_GetSimulatorFieldMetadata(
+          simulatorModel,i,&sim_lines,&sim_field);
+      if (0 == strcmp(sim_field,"model-init")) {
+        for (int j=0; j < sim_lines; ++j) {
+          KIM_SimulatorModel_GetSimulatorFieldLine(
+              simulatorModel,i,j,&sim_value);
+          input->one(sim_value);
+        }
+        break;
+      }
+    }
+
+    // reset template map.
+    KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel);
+  }
+
+  // End output to log file
+  kim_init_log_delimiter("end");
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void KimInit::kim_init_log_delimiter(std::string const begin_end) const
+{
+  if (comm->me == 0) {
+    std::string mesg;
+    if (begin_end == "begin")
+      mesg =
+          "#=== BEGIN kim-init ==========================================\n";
+    else if (begin_end == "end")
+      mesg =
+          "#=== END kim-init ============================================\n\n";
+
+    input->write_echo(mesg.c_str());
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void KimInit::do_variables(char *user_units, char *model_units)
+{
+  char *from = user_units, *to = model_units;
+  Variable *variable = input->variable;
+
+  // refuse conversion from or to reduced units
+
+  if ((strcmp(from,"lj") == 0) || (strcmp(to,"lj") == 0))
+    error->all(FLERR,"Cannot set up conversion variables for 'lj' units");
+
+  // get index to internal style variables. create, if needed.
+  // set conversion factors for newly created variables.
+  double conversion_factor;
+  int ier;
+  char *args[3];
+  std::string var_str;
+  args[1] = (char *)"internal";
+  args[2] = (char *)"1.0";
+  int v_unit;
+  int const nunits = 14;
+  char *units[nunits] = {(char *)"mass",
+                         (char *)"distance",
+                         (char *)"time",
+                         (char *)"energy",
+                         (char *)"velocity",
+                         (char *)"force",
+                         (char *)"torque",
+                         (char *)"temperature",
+                         (char *)"pressure",
+                         (char *)"viscosity",
+                         (char *)"charge",
+                         (char *)"dipole",
+                         (char *)"efield",
+                         (char *)"density"};
+
+  if (comm->me == 0) {
+    std::string mesg("# Conversion factors from ");
+    mesg += from;
+    mesg += " to ";
+    mesg += to;
+    mesg += ":\n";
+    input->write_echo(mesg.c_str());
+  }
+
+  for (int i = 0; i < nunits; i++) {
+    var_str = std::string("_u_") + std::string(units[i]);
+    args[0] = (char *)var_str.c_str();
+    v_unit = variable->find(args[0]);
+    if (v_unit < 0) {
+      variable->set(3,args);
+      v_unit = variable->find(args[0]);
+    }
+    ier = lammps_unit_conversion(units[i],
+                                 from,
+                                 to,
+                                 conversion_factor);
+    if (ier != 0) {
+      std::string err = std::string("Unable to obtain conversion factor: ") +
+                        "unit = " + units[i] + "; "
+                        "from = " + from + "; "
+                        "to = " + to + ".";
+      error->all(FLERR,err.c_str());
+    }
+    variable->internal_set(v_unit,conversion_factor);
+    if (comm->me == 0) {
+      std::stringstream mesg;
+      mesg << "variable " << std::setw(15) << std::left << var_str
+           << " internal "
+           << std::setprecision(12) << std::scientific << conversion_factor
+           << std::endl;
+      input->write_echo(mesg.str().c_str());
+    }
+  }
+  if (comm->me == 0) input->write_echo("#\n");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void KimInit::write_log_cite(char * model_name)
+{
+  KIM_Collections * coll;
+  int err = KIM_Collections_Create(&coll);
+  if (err) return;
+
+  int extent;
+  if (model_type == MO)
+  {
+    err = KIM_Collections_CacheListOfItemMetadataFiles(
+        coll,KIM_COLLECTION_ITEM_TYPE_portableModel,model_name,&extent);
+  }
+  else if (model_type == SM)
+  {
+    err = KIM_Collections_CacheListOfItemMetadataFiles(
+        coll,KIM_COLLECTION_ITEM_TYPE_simulatorModel,model_name,&extent);
+  }
+  else
+  {
+    error->all(FLERR,"Unknown model type.");
+  }
+
+  if (err)
+  {
+    KIM_Collections_Destroy(&coll);
+    return;
+  }
+
+  for (int i = 0; i < extent;++i)
+  {
+    char const * fileName;
+    int availableAsString;
+    char const * fileString;
+    err = KIM_Collections_GetItemMetadataFile(
+        coll,i,&fileName,NULL,NULL,&availableAsString,&fileString);
+    if (err) continue;
+
+    if (0 == strncmp("kimcite",fileName,7))
+    {
+      if ((lmp->citeme) && (availableAsString)) lmp->citeme->add(fileString);
+    }
+  }
+
+  KIM_Collections_Destroy(&coll);
+}
diff --git a/src/KIM/kim_init.h b/src/KIM/kim_init.h
new file mode 100644
index 0000000000..2b5dc520c7
--- /dev/null
+++ b/src/KIM/kim_init.h
@@ -0,0 +1,131 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors: Axel Kohlmeyer (Temple U),
+                         Ryan S. Elliott (UMN)
+                         Ellad B. Tadmor (UMN)
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   This program is free software; you can redistribute it and/or modify it
+   under the terms of the GNU General Public License as published by the Free
+   Software Foundation; either version 2 of the License, or (at your option)
+   any later version.
+
+   This program is distributed in the hope that it will be useful, but WITHOUT
+   ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+   FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+   more details.
+
+   You should have received a copy of the GNU General Public License along with
+   this program; if not, see <https://www.gnu.org/licenses>.
+
+   Linking LAMMPS statically or dynamically with other modules is making a
+   combined work based on LAMMPS. Thus, the terms and conditions of the GNU
+   General Public License cover the whole combination.
+
+   In addition, as a special exception, the copyright holders of LAMMPS give
+   you permission to combine LAMMPS with free software programs or libraries
+   that are released under the GNU LGPL and with code included in the standard
+   release of the "kim-api" under the CDDL (or modified versions of such code,
+   with unchanged license). You may copy and distribute such a system following
+   the terms of the GNU GPL for LAMMPS and the licenses of the other code
+   concerned, provided that you include the source code of that other code
+   when and as the GNU GPL requires distribution of source code.
+
+   Note that people who make modified versions of LAMMPS are not obligated to
+   grant this special exception for their modified versions; it is their choice
+   whether to do so. The GNU General Public License gives permission to release
+   a modified version without this exception; this exception also makes it
+   possible to release a modified version which carries forward this exception.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Designed for use with the kim-api-2.1.0 (and newer) package
+------------------------------------------------------------------------- */
+
+#ifdef COMMAND_CLASS
+
+CommandStyle(kim_init,KimInit)
+
+#else
+
+#ifndef LMP_KIM_INIT_H
+#define LMP_KIM_INIT_H
+
+#include "pointers.h"
+#include <string>
+
+namespace LAMMPS_NS {
+
+class KimInit : protected Pointers {
+ public:
+  KimInit(class LAMMPS *lmp) : Pointers(lmp) {};
+  void command(int, char **);
+ private:
+  enum model_type_enum {MO, SM};
+  model_type_enum model_type;
+  bool unit_conversion_mode;
+
+  void determine_model_type_and_units(char *, char *, char **);
+  void write_log_cite(char *);
+  void do_init(char *, char *, char *);
+  void do_variables(char*, char*);
+  void kim_init_log_delimiter(std::string const begin_end) const;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal kim_init command
+
+Incorrect number or kind of arguments to kim_init.
+
+E: Must use 'kim_init' command before simulation box is defined
+
+Self-explanatory.
+
+E: KIM Model does not support the requested unit system
+
+Self-explanatory.
+
+E: KIM Model does not support any lammps unit system
+
+Self-explanatory.
+
+E: KIM model name not found
+
+Self-explanatory.
+
+E: Incompatible KIM Simulator Model
+
+The requested KIM Simulator Model was defined for a different MD code
+and thus is not compatible with LAMMPS.
+
+E: Incompatible units for KIM Simulator Model
+
+The selected unit style is not compatible with the requested KIM
+Simulator Model.
+
+E: KIM Simulator Model has no Model definition
+
+There is no model definition (key: model-defn) in the KIM Simulator
+Model.  Please contact the OpenKIM database maintainers to verify
+and potentially correct this.
+
+*/
diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp
new file mode 100644
index 0000000000..7dbe523033
--- /dev/null
+++ b/src/KIM/kim_interactions.cpp
@@ -0,0 +1,387 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors: Axel Kohlmeyer (Temple U),
+                         Ryan S. Elliott (UMN)
+                         Ellad B. Tadmor (UMN)
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   This program is free software; you can redistribute it and/or modify it
+   under the terms of the GNU General Public License as published by the Free
+   Software Foundation; either version 2 of the License, or (at your option)
+   any later version.
+
+   This program is distributed in the hope that it will be useful, but WITHOUT
+   ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+   FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+   more details.
+
+   You should have received a copy of the GNU General Public License along with
+   this program; if not, see <https://www.gnu.org/licenses>.
+
+   Linking LAMMPS statically or dynamically with other modules is making a
+   combined work based on LAMMPS. Thus, the terms and conditions of the GNU
+   General Public License cover the whole combination.
+
+   In addition, as a special exception, the copyright holders of LAMMPS give
+   you permission to combine LAMMPS with free software programs or libraries
+   that are released under the GNU LGPL and with code included in the standard
+   release of the "kim-api" under the CDDL (or modified versions of such code,
+   with unchanged license). You may copy and distribute such a system following
+   the terms of the GNU GPL for LAMMPS and the licenses of the other code
+   concerned, provided that you include the source code of that other code
+   when and as the GNU GPL requires distribution of source code.
+
+   Note that people who make modified versions of LAMMPS are not obligated to
+   grant this special exception for their modified versions; it is their choice
+   whether to do so. The GNU General Public License gives permission to release
+   a modified version without this exception; this exception also makes it
+   possible to release a modified version which carries forward this exception.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Designed for use with the kim-api-2.1.0 (and newer) package
+------------------------------------------------------------------------- */
+
+#include "kim_interactions.h"
+#include <cstring>
+#include <string>
+#include <sstream>
+#include "error.h"
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "modify.h"
+#include "update.h"
+#include "universe.h"
+#include "input.h"
+#include "variable.h"
+#include "fix_store_kim.h"
+
+extern "C" {
+#include "KIM_SimulatorHeaders.h"
+}
+
+#define SNUM(x)                                                \
+  static_cast<std::ostringstream const &>(std::ostringstream() \
+                                          << std::dec << x).str()
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+void KimInteractions::command(int narg, char **arg)
+{
+  if (narg < 1) error->all(FLERR,"Illegal kim_interactions command");
+
+  if (!domain->box_exist)
+    error->all(FLERR,"Must use 'kim_interactions' command after "
+                     "simulation box is defined");
+  do_setup(narg,arg);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void KimInteractions::kim_interactions_log_delimiter(
+    std::string const begin_end) const
+{
+  if (comm->me == 0) {
+    std::string mesg;
+    if (begin_end == "begin")
+      mesg =
+          "#=== BEGIN kim_interactions ==================================\n";
+    else if (begin_end == "end")
+      mesg =
+          "#=== END kim_interactions ====================================\n\n";
+
+    input->write_echo(mesg.c_str());
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void KimInteractions::do_setup(int narg, char **arg)
+{
+  bool fixed_types;
+  if ((narg == 1) && (0 == strcmp("fixed_types",arg[0]))) {
+    fixed_types = true;
+  }
+  else if (narg != atom->ntypes) {
+    error->all(FLERR,"Illegal kim_interactions command");
+  }
+  else {
+    fixed_types = false;
+  }
+
+  char *model_name = NULL;
+  KIM_SimulatorModel *simulatorModel(NULL);
+
+  // check if we had a kim_init command by finding fix STORE/KIM
+  // retrieve model name and pointer to simulator model class instance.
+  // validate model name if not given as NULL.
+
+  int ifix = modify->find_fix("KIM_MODEL_STORE");
+  if (ifix >= 0) {
+    FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix];
+    model_name = (char *)fix_store->getptr("model_name");
+    simulatorModel = (KIM_SimulatorModel *)fix_store->getptr("simulator_model");
+  } else error->all(FLERR,"Must use 'kim_init' before 'kim_interactions'");
+
+  // Begin output to log file
+  kim_interactions_log_delimiter("begin");
+
+  if (simulatorModel) {
+
+    if (!fixed_types) {
+      std::string delimiter("");
+      std::string atom_type_sym_list;
+      std::string atom_type_num_list;
+
+      for (int i = 0; i < narg; i++)
+      {
+        atom_type_sym_list += delimiter + arg[i];
+        atom_type_num_list += delimiter + SNUM(species_to_atomic_no(arg[i]));
+        delimiter = " ";
+      }
+
+      KIM_SimulatorModel_AddTemplateMap(
+          simulatorModel,"atom-type-sym-list",atom_type_sym_list.c_str());
+      KIM_SimulatorModel_AddTemplateMap(
+          simulatorModel,"atom-type-num-list",atom_type_num_list.c_str());
+      KIM_SimulatorModel_CloseTemplateMap(simulatorModel);
+
+      int len = strlen(atom_type_sym_list.c_str())+1;
+      char *strbuf = new char[len];
+      char *strword;
+
+      // validate species selection
+
+      int sim_num_species;
+      bool species_is_supported;
+      char const *sim_species;
+      KIM_SimulatorModel_GetNumberOfSupportedSpecies(
+          simulatorModel,&sim_num_species);
+      strcpy(strbuf,atom_type_sym_list.c_str());
+      strword = strtok(strbuf," \t");
+      while (strword) {
+        species_is_supported = false;
+        if (strcmp(strword,"NULL") == 0) continue;
+        for (int i=0; i < sim_num_species; ++i) {
+          KIM_SimulatorModel_GetSupportedSpecies(simulatorModel,i,&sim_species);
+          if (strcmp(sim_species,strword) == 0)
+            species_is_supported = true;
+        }
+        if (!species_is_supported) {
+          std::string msg("Species '");
+          msg += strword;
+          msg += "' is not supported by this KIM Simulator Model";
+          error->all(FLERR,msg.c_str());
+        }
+        strword = strtok(NULL," \t");
+      }
+      delete[] strbuf;
+    }
+    else
+    {
+      KIM_SimulatorModel_CloseTemplateMap(simulatorModel);
+    }
+
+    // check if units are unchanged
+
+    int sim_fields, sim_lines;
+    const char *sim_field, *sim_value;
+    KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields);
+    for (int i=0; i < sim_fields; ++i) {
+      KIM_SimulatorModel_GetSimulatorFieldMetadata(
+          simulatorModel,i,&sim_lines,&sim_field);
+
+      if (0 == strcmp(sim_field,"units")) {
+        KIM_SimulatorModel_GetSimulatorFieldLine(simulatorModel,i,0,&sim_value);
+        if (0 != strcmp(sim_value,update->unit_style))
+          error->all(FLERR,"Incompatible units for KIM Simulator Model");
+      }
+    }
+
+    int sim_model_idx=-1;
+    for (int i=0; i < sim_fields; ++i) {
+      KIM_SimulatorModel_GetSimulatorFieldMetadata(
+          simulatorModel,i,&sim_lines,&sim_field);
+      if (0 == strcmp(sim_field,"model-defn")) {
+        sim_model_idx = i;
+        for (int j=0; j < sim_lines; ++j) {
+          KIM_SimulatorModel_GetSimulatorFieldLine(
+              simulatorModel,sim_model_idx,j,&sim_value);
+          input->one(sim_value);
+        }
+      }
+    }
+
+    if (sim_model_idx < 0)
+      error->all(FLERR,"KIM Simulator Model has no Model definition");
+
+    KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel);
+
+  } else {
+
+    // not a simulator model. issue pair_style and pair_coeff commands.
+
+    if (fixed_types)
+      error->all(FLERR,"fixed_types cannot be used with a KIM Portable Model");
+
+    // NOTE: all references to arg must appear before calls to input->one()
+    // as that will reset the argument vector.
+
+    std::string cmd1("pair_style kim ");
+    cmd1 += model_name;
+
+    std::string cmd2("pair_coeff * * ");
+    for (int i=0; i < narg; ++i) {
+      cmd2 += arg[i];
+      cmd2 += " ";
+    }
+
+    input->one(cmd1.c_str());
+    input->one(cmd2.c_str());
+  }
+
+  // End output to log file
+  kim_interactions_log_delimiter("end");
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+int KimInteractions::species_to_atomic_no(std::string const species) const
+{
+  if (species == "H") return 1;
+  else if (species == "He") return 2;
+  else if (species == "Li") return 3;
+  else if (species == "Be") return 4;
+  else if (species == "B") return 5;
+  else if (species == "C") return 6;
+  else if (species == "N") return 7;
+  else if (species == "O") return 8;
+  else if (species == "F") return 9;
+  else if (species == "Ne") return 10;
+  else if (species == "Na") return 11;
+  else if (species == "Mg") return 12;
+  else if (species == "Al") return 13;
+  else if (species == "Si") return 14;
+  else if (species == "P") return 15;
+  else if (species == "S") return 16;
+  else if (species == "Cl") return 17;
+  else if (species == "Ar") return 18;
+  else if (species == "K") return 19;
+  else if (species == "Ca") return 20;
+  else if (species == "Sc") return 21;
+  else if (species == "Ti") return 22;
+  else if (species == "V") return 23;
+  else if (species == "Cr") return 24;
+  else if (species == "Mn") return 25;
+  else if (species == "Fe") return 26;
+  else if (species == "Co") return 27;
+  else if (species == "Ni") return 28;
+  else if (species == "Cu") return 29;
+  else if (species == "Zn") return 30;
+  else if (species == "Ga") return 31;
+  else if (species == "Ge") return 32;
+  else if (species == "As") return 33;
+  else if (species == "Se") return 34;
+  else if (species == "Br") return 35;
+  else if (species == "Kr") return 36;
+  else if (species == "Rb") return 37;
+  else if (species == "Sr") return 38;
+  else if (species == "Y") return 39;
+  else if (species == "Zr") return 40;
+  else if (species == "Nb") return 41;
+  else if (species == "Mo") return 42;
+  else if (species == "Tc") return 43;
+  else if (species == "Ru") return 44;
+  else if (species == "Rh") return 45;
+  else if (species == "Pd") return 46;
+  else if (species == "Ag") return 47;
+  else if (species == "Cd") return 48;
+  else if (species == "In") return 49;
+  else if (species == "Sn") return 50;
+  else if (species == "Sb") return 51;
+  else if (species == "Te") return 52;
+  else if (species == "I") return 53;
+  else if (species == "Xe") return 54;
+  else if (species == "Cs") return 55;
+  else if (species == "Ba") return 56;
+  else if (species == "La") return 57;
+  else if (species == "Ce") return 58;
+  else if (species == "Pr") return 59;
+  else if (species == "Nd") return 60;
+  else if (species == "Pm") return 61;
+  else if (species == "Sm") return 62;
+  else if (species == "Eu") return 63;
+  else if (species == "Gd") return 64;
+  else if (species == "Tb") return 65;
+  else if (species == "Dy") return 66;
+  else if (species == "Ho") return 67;
+  else if (species == "Er") return 68;
+  else if (species == "Tm") return 69;
+  else if (species == "Yb") return 70;
+  else if (species == "Lu") return 71;
+  else if (species == "Hf") return 72;
+  else if (species == "Ta") return 73;
+  else if (species == "W") return 74;
+  else if (species == "Re") return 75;
+  else if (species == "Os") return 76;
+  else if (species == "Ir") return 77;
+  else if (species == "Pt") return 78;
+  else if (species == "Au") return 79;
+  else if (species == "Hg") return 80;
+  else if (species == "Tl") return 81;
+  else if (species == "Pb") return 82;
+  else if (species == "Bi") return 83;
+  else if (species == "Po") return 84;
+  else if (species == "At") return 85;
+  else if (species == "Rn") return 86;
+  else if (species == "Fr") return 87;
+  else if (species == "Ra") return 88;
+  else if (species == "Ac") return 89;
+  else if (species == "Th") return 90;
+  else if (species == "Pa") return 91;
+  else if (species == "U") return 92;
+  else if (species == "Np") return 93;
+  else if (species == "Pu") return 94;
+  else if (species == "Am") return 95;
+  else if (species == "Cm") return 96;
+  else if (species == "Bk") return 97;
+  else if (species == "Cf") return 98;
+  else if (species == "Es") return 99;
+  else if (species == "Fm") return 100;
+  else if (species == "Md") return 101;
+  else if (species == "No") return 102;
+  else if (species == "Lr") return 103;
+  else if (species == "Rf") return 104;
+  else if (species == "Db") return 105;
+  else if (species == "Sg") return 106;
+  else if (species == "Bh") return 107;
+  else if (species == "Hs") return 108;
+  else if (species == "Mt") return 109;
+  else if (species == "Ds") return 110;
+  else if (species == "Rg") return 111;
+  else if (species == "Cn") return 112;
+  else if (species == "Nh") return 113;
+  else if (species == "Fl") return 114;
+  else if (species == "Mc") return 115;
+  else if (species == "Lv") return 116;
+  else if (species == "Ts") return 117;
+  else if (species == "Og") return 118;
+  else return -1;
+}
diff --git a/src/KIM/kim_interactions.h b/src/KIM/kim_interactions.h
new file mode 100644
index 0000000000..8172004d53
--- /dev/null
+++ b/src/KIM/kim_interactions.h
@@ -0,0 +1,117 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors: Axel Kohlmeyer (Temple U),
+                         Ryan S. Elliott (UMN)
+                         Ellad B. Tadmor (UMN)
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   This program is free software; you can redistribute it and/or modify it
+   under the terms of the GNU General Public License as published by the Free
+   Software Foundation; either version 2 of the License, or (at your option)
+   any later version.
+
+   This program is distributed in the hope that it will be useful, but WITHOUT
+   ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+   FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+   more details.
+
+   You should have received a copy of the GNU General Public License along with
+   this program; if not, see <https://www.gnu.org/licenses>.
+
+   Linking LAMMPS statically or dynamically with other modules is making a
+   combined work based on LAMMPS. Thus, the terms and conditions of the GNU
+   General Public License cover the whole combination.
+
+   In addition, as a special exception, the copyright holders of LAMMPS give
+   you permission to combine LAMMPS with free software programs or libraries
+   that are released under the GNU LGPL and with code included in the standard
+   release of the "kim-api" under the CDDL (or modified versions of such code,
+   with unchanged license). You may copy and distribute such a system following
+   the terms of the GNU GPL for LAMMPS and the licenses of the other code
+   concerned, provided that you include the source code of that other code
+   when and as the GNU GPL requires distribution of source code.
+
+   Note that people who make modified versions of LAMMPS are not obligated to
+   grant this special exception for their modified versions; it is their choice
+   whether to do so. The GNU General Public License gives permission to release
+   a modified version without this exception; this exception also makes it
+   possible to release a modified version which carries forward this exception.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Designed for use with the kim-api-2.1.0 (and newer) package
+------------------------------------------------------------------------- */
+
+#ifdef COMMAND_CLASS
+
+CommandStyle(kim_interactions,KimInteractions)
+
+#else
+
+#ifndef LMP_KIM_INTERACTIONS_H
+#define LMP_KIM_INTERACTIONS_H
+
+#include "pointers.h"
+#include <string>
+
+namespace LAMMPS_NS {
+
+class KimInteractions : protected Pointers {
+ public:
+  KimInteractions(class LAMMPS *lmp) : Pointers(lmp) {};
+  void command(int, char **);
+ private:
+  void do_setup(int, char **);
+  int species_to_atomic_no(std::string const species) const;
+  void kim_interactions_log_delimiter(std::string const begin_end) const;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal kim_interactions command
+
+Incorrect number or kind of arguments to kim_interactions.
+
+E: Must use 'kim_interactions' command after simulation box is defined
+
+Self-explanatory.
+
+E: Must use 'kim_init' command before 'kim_interactions'
+
+Self-explanatory.
+
+E: Species XXX is not supported by this KIM Simulator Model
+
+The kim_interactions command was referencing a species that is not
+present in the requested KIM Simulator Model.
+
+E: Incompatible units for KIM Simulator Model
+
+The selected unit style is not compatible with the requested KIM
+Simulator Model.
+
+E: KIM Simulator Model has no Model definition
+
+There is no model definition (key: model-defn) in the KIM Simulator
+Model.  Please contact the OpenKIM database maintainers to verify
+and potentially correct this.
+
+*/
diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp
index fedc976110..8ceefeceaf 100644
--- a/src/KIM/kim_query.cpp
+++ b/src/KIM/kim_query.cpp
@@ -11,7 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-
 /* ----------------------------------------------------------------------
    Contributing authors: Axel Kohlmeyer (Temple U),
                          Ryan S. Elliott (UMN)
@@ -52,17 +51,22 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Designed for use with the kim-api-2.0.2 (and newer) package
+   Designed for use with the kim-api-2.1.0 (and newer) package
 ------------------------------------------------------------------------- */
 
+#include "kim_query.h"
 #include <mpi.h>
 #include <cstring>
 #include <string>
-#include "kim_query.h"
+#include <sstream>
 #include "comm.h"
 #include "error.h"
 #include "input.h"
+#include "modify.h"
 #include "variable.h"
+#include "version.h"
+#include "info.h"
+#include "fix_store_kim.h"
 
 #if defined(LMP_KIM_CURL)
 #include <sys/types.h>
@@ -78,7 +82,7 @@ struct WriteBuf {
   size_t sizeleft;
 };
 
-static char *do_query(char *, int, char **, int, MPI_Comm);
+static char *do_query(char *, char *, int, char **, int, MPI_Comm);
 static size_t write_callback(void *, size_t, size_t, void *);
 
 #endif
@@ -91,31 +95,79 @@ void KimQuery::command(int narg, char **arg)
 
   if (narg < 2) error->all(FLERR,"Illegal kim_query command");
 
+  // check if we had a kim_init command by finding fix STORE/KIM
+  // retrieve model name.
+  char * model_name;
+
+  int ifix = modify->find_fix("KIM_MODEL_STORE");
+  if (ifix >= 0) {
+    FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix];
+    model_name = (char *)fix_store->getptr("model_name");
+  } else error->all(FLERR,"Must use 'kim_init' before 'kim_query'");
+
+
   varname = arg[0];
+  bool split = false;
+  if (0 == strcmp("split",arg[1])) {
+    if (narg == 2) error->all(FLERR,"Illegal kim_query command");
+    split = true;
+    arg++;
+    narg--;
+  }
   function = arg[1];
+  for (int i = 2; i < narg; ++i)
+  {
+    if (0 == strncmp("model=",arg[i], 6)) {
+      error->all(FLERR,"Illegal 'model' key in kim_query command");
+    }
+  }
+
 
 #if defined(LMP_KIM_CURL)
 
-  value = do_query(function, narg-2, arg+2, comm->me, world);
+  value = do_query(function, model_name, narg-2, arg+2, comm->me, world);
 
   // check for valid result
   // on error the content of "value" is a '\0' byte
   // as the first element, and then the error message
   // that was returned by the web server
 
+  char errmsg[1024];
   if (0 == strlen(value)) {
-    char errmsg[512];
-
     sprintf(errmsg,"OpenKIM query failed: %s",value+1);
-        error->all(FLERR,errmsg);
+    error->all(FLERR,errmsg);
+  } else if (0 == strcmp(value,"EMPTY")) {
+    sprintf(errmsg,"OpenKIM query returned no results");
+    error->all(FLERR,errmsg);
   }
 
+  kim_query_log_delimiter("begin");
   char **varcmd = new char*[3];
-  varcmd[0] = varname;
-  varcmd[1] = (char *) "string";
-  varcmd[2] = value;
+  if (split) {
+    int counter = 1;
+    std::stringstream ss(value);
+    std::string token;
+    varcmd[1] = (char *) "string";
 
-  input->variable->set(3,varcmd);
+    while(std::getline(ss, token, ',')) {
+      token.erase(0,token.find_first_not_of(" \n\r\t"));  // ltrim
+      token.erase(token.find_last_not_of(" \n\r\t") + 1);  // rtrim
+      std::stringstream splitname;
+      splitname << varname << "_" << counter++;
+      varcmd[0] = const_cast<char *>(splitname.str().c_str());
+      varcmd[2] = const_cast<char *>(token.c_str());
+      input->variable->set(3,varcmd);
+      echo_var_assign(splitname.str(), varcmd[2]);
+    }
+  } else {
+    varcmd[0] = varname;
+    varcmd[1] = (char *) "string";
+    varcmd[2] = value;
+    input->variable->set(3,varcmd);
+
+    echo_var_assign(varname, value);
+  }
+  kim_query_log_delimiter("end");
 
   delete[] varcmd;
   delete[] value;
@@ -148,7 +200,8 @@ size_t write_callback(void *data, size_t size, size_t nmemb, void *userp)
   return 0; // done
 }
 
-char *do_query(char *qfunction, int narg, char **arg, int rank, MPI_Comm comm)
+char *do_query(char *qfunction, char * model_name, int narg, char **arg,
+               int rank, MPI_Comm comm)
 {
   char value[512], *retval;
 
@@ -174,6 +227,9 @@ char *do_query(char *qfunction, int narg, char **arg, int rank, MPI_Comm comm)
       url += qfunction;
 
       std::string query(arg[0]);
+      query += "&model=[\"";
+      query += model_name;
+      query += "\"]";
       for (int i=1; i < narg; ++i) {
         query += '&';
         query += arg[i];
@@ -188,6 +244,10 @@ char *do_query(char *qfunction, int narg, char **arg, int rank, MPI_Comm comm)
       curl_easy_setopt(handle, CURLOPT_SSL_VERIFYPEER, 0L);
       curl_easy_setopt(handle, CURLOPT_SSL_VERIFYHOST, 0L);
 #endif
+      std::string user_agent = std::string("kim_query--LAMMPS/")
+                               + LAMMPS_VERSION
+                               + " (" + Info::get_os_info() + ")";
+      curl_easy_setopt(handle, CURLOPT_USERAGENT, user_agent.c_str());
 
       curl_easy_setopt(handle, CURLOPT_URL, url.c_str());
       curl_easy_setopt(handle, CURLOPT_FOLLOWLOCATION, 1L);
@@ -217,9 +277,19 @@ char *do_query(char *qfunction, int narg, char **arg, int rank, MPI_Comm comm)
 
   if (value[0] == '[') {
     int len = strlen(value)-1;
-    retval = new char[len];
-    value[len] = '\0';
-    strcpy(retval,value+1);
+    if (value[len] == ']') {
+      retval = new char[len];
+      value[len] = '\0';
+      if (0 == strcmp(value+1, "")) {
+        strcpy(retval,"EMPTY");
+      }
+      else
+        strcpy(retval,value+1);
+    } else {
+      retval = new char[len+2];
+      retval[0] = '\0';
+      strcpy(retval+1,value);
+    }
   } else if (value[0] == '\0') {
     int len = strlen(value+1)+2;
     retval = new char[len];
@@ -227,11 +297,41 @@ char *do_query(char *qfunction, int narg, char **arg, int rank, MPI_Comm comm)
     strcpy(retval+1,value+1);
   } else {
     // unknown response type. we should not get here.
-    // copy response without modifications.
-    int len = strlen(value)+1;
+    // we return an "empty" string but add error message after it
+    int len = strlen(value)+2;
     retval = new char[len];
-    strcpy(retval,value);
+    retval[0] = '\0';
+    strcpy(retval+1,value);
   }
   return retval;
 }
 #endif
+
+/* ---------------------------------------------------------------------- */
+
+void KimQuery::kim_query_log_delimiter(std::string const begin_end) const
+{
+  if (comm->me == 0) {
+    std::string mesg;
+    if (begin_end == "begin")
+      mesg =
+          "#=== BEGIN kim-query =========================================\n";
+    else if (begin_end == "end")
+      mesg =
+          "#=== END kim-query ===========================================\n\n";
+
+    input->write_echo(mesg.c_str());
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void KimQuery::echo_var_assign(std::string const & name,
+                               std::string const & value) const
+{
+  if (comm->me == 0) {
+    std::string mesg;
+    mesg += "variable " + name + " string " + value + "\n";
+    input->write_echo(mesg.c_str());
+  }
+}
diff --git a/src/KIM/kim_query.h b/src/KIM/kim_query.h
index 3644e4519b..33a37f5131 100644
--- a/src/KIM/kim_query.h
+++ b/src/KIM/kim_query.h
@@ -51,7 +51,7 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Designed for use with the kim-api-2.0.2 (and newer) package
+   Designed for use with the kim-api-2.1.0 (and newer) package
 ------------------------------------------------------------------------- */
 
 #ifdef COMMAND_CLASS
@@ -64,6 +64,7 @@ CommandStyle(kim_query,KimQuery)
 #define LMP_KIM_QUERY_H
 
 #include "pointers.h"
+#include <string>
 
 namespace LAMMPS_NS {
 
@@ -71,7 +72,10 @@ class KimQuery : protected Pointers {
  public:
   KimQuery(class LAMMPS *lmp) : Pointers(lmp) {};
   void command(int, char **);
-
+ private:
+  void kim_query_log_delimiter(std::string const begin_end) const;
+  void echo_var_assign(std::string const & name, std::string const & value)
+  const;
 };
 
 }
diff --git a/src/KIM/kim_units.cpp b/src/KIM/kim_units.cpp
new file mode 100644
index 0000000000..45f9b81a35
--- /dev/null
+++ b/src/KIM/kim_units.cpp
@@ -0,0 +1,1411 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors: Ellad B. Tadmor (UMN)
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   This program is free software; you can redistribute it and/or modify it
+   under the terms of the GNU General Public License as published by the Free
+   Software Foundation; either version 2 of the License, or (at your option)
+   any later version.
+
+   This program is distributed in the hope that it will be useful, but WITHOUT
+   ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+   FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+   more details.
+
+   You should have received a copy of the GNU General Public License along with
+   this program; if not, see <https://www.gnu.org/licenses>.
+
+   Linking LAMMPS statically or dynamically with other modules is making a
+   combined work based on LAMMPS. Thus, the terms and conditions of the GNU
+   General Public License cover the whole combination.
+
+   In addition, as a special exception, the copyright holders of LAMMPS give
+   you permission to combine LAMMPS with free software programs or libraries
+   that are released under the GNU LGPL and with code included in the standard
+   release of the "kim-api" under the CDDL (or modified versions of such code,
+   with unchanged license). You may copy and distribute such a system following
+   the terms of the GNU GPL for LAMMPS and the licenses of the other code
+   concerned, provided that you include the source code of that other code
+   when and as the GNU GPL requires distribution of source code.
+
+   Note that people who make modified versions of LAMMPS are not obligated to
+   grant this special exception for their modified versions; it is their choice
+   whether to do so. The GNU General Public License gives permission to release
+   a modified version without this exception; this exception also makes it
+   possible to release a modified version which carries forward this exception.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Designed for use with the kim-api-2.0.2 (and newer) package
+------------------------------------------------------------------------- */
+
+#include <iostream>
+#include <math.h>
+#include <string>
+#include <map>
+using namespace std;
+
+namespace
+{
+
+// Constants of nature and basic conversion factors
+// Source: https://physics.nist.gov/cuu/Constants/Table/allascii.txt
+//         Working with NIST values even when there are newer values for
+//         compatibility with LAMMPS
+
+/*----------------------
+   Fundamental constants
+------------------------ */
+double const boltz_si = 1.38064852e-23;  // [J K^-1] Boltzmann's factor
+                                         //   (NIST value)
+double const Nav = 6.022140857e23;       // [unitless] Avogadro's number
+                                         //   (NIST value)
+// double const Nav = 6.02214076e23;     // [unitless] Avogadro's number
+                                         //   (official value May 2019)
+double const me_si = 9.10938356e-31;     // [kg] electron rest mass
+                                         //   (NIST value)
+// double me_si = 9.10938291e-31;        // [kg] electron rest mass
+double const e_si = 1.6021766208e-19;    // [C] elementary charge
+                                         //   (charge of an electron/proton)
+                                         //   (NIST value)
+
+/*----------------------
+   Distance units
+------------------------ */
+double const bohr_si = 5.2917721067e-11;  // [m] Bohr unit (distance between
+                                          //   nucleus and electron in H)
+                                          //   (NIST value)
+double const angstrom_si = 1e-10;         // [m] Angstrom
+double const centimeter_si = 1e-2;        // [m] centimeter
+double const micrometer_si = 1e-6;        // [m] micrometer (micron)
+double const nanometer_si = 1e-9;         // [m] nanometer
+
+/*----------------------
+   Mass units
+------------------------ */
+double const gram_per_mole_si = 1e-3/Nav;  // [kg] gram per mole
+double const amu_si = 1e-3/Nav;            // [kg] atomic mass unit (molecular
+                                           //   weight) For example, the mean
+                                           //   molecular weight of water
+                                           //   is 18.015 atomic mass units
+                                           //   (amu), so one mole of water
+                                           //   weight 18.015 grams.
+double const gram_si = 1e-3;               // [kg] gram
+double const picogram_si = 1e-15;          // [kg] picogram
+double const attogram_si = 1e-21;          // [kg[ attogram
+
+/*----------------------
+   Time units
+------------------------ */
+double const atu_si = 2.418884326509e-17;  // [s] atomic time unit
+                                           //   ( = hbar/E_h where E_h is the
+                                           //   Hartree energy) (NIST value)
+double const atu_electron_si = atu_si*sqrt(amu_si/me_si);
+                                          // [s] atomic time unit
+                                          //   used in electron system (see https://sourceforge.net/p/lammps/mailman/lammps-users/thread/BCA2BDB2-BA03-4280-896F-1E6120EF47B2%40caltech.edu/)
+double const microsecond_si = 1e-6;        // [s] microsecond
+double const nanosecond_si = 1e-9;         // [s] nanosecond
+double const picosecond_si = 1e-12;        // [s] picosecond
+double const femtosecond_si = 1e-15;       // [s] femtosecond
+
+/*----------------------
+   Density units
+------------------------ */
+double const gram_per_centimetercu_si =
+             gram_si/pow(centimeter_si,3);  // [kg/m^3] gram/centimeter^3
+double const amu_per_bohrcu_si = amu_si/pow(bohr_si,3);  // [kg/m^3] amu/bohr^3
+double const picogram_per_micrometercu_si =
+             picogram_si/pow(micrometer_si,3); // [kg/m^3] picogram/micrometer^3
+double const attogram_per_nanometercu_si =
+             attogram_si/pow(nanometer_si,3);  // [kg/m^3] attogram/nanometer^3
+
+/*----------------------
+   Energy/torque units
+------------------------ */
+double const kcal_si = 4184.0;              // [J] kilocalorie (heat energy
+                                            //   involved in warming up one
+                                            //   kilogram of water by one
+                                            //   degree Kelvin)
+double const ev_si = 1.6021766208e-19;      // [J] electon volt (amount of
+                                            //   energy gained or lost by the
+                                            //   charge of a single electron
+                                            //   moving across an electric
+                                            //   potential difference of one
+                                            //   volt.) (NIST value)
+double const hartree_si = 4.359744650e-18;  // [J] Hartree (approximately the
+                                            //   electric potential energy of
+                                            //   the hydrogen atom in its
+                                            //   ground state) (NIST value)
+double const kcal_per_mole_si = kcal_si/Nav;// [J] kcal/mole
+double const erg_si = 1e-7;                 // [J] erg
+double const dyne_centimeter_si = 1e-7;     // [J[ dyne*centimeter
+double const picogram_micrometersq_per_microsecondsq_si =
+             picogram_si*pow(micrometer_si,2)/pow(microsecond_si,2);
+                                            // [J] picogram*micrometer^2/
+                                            //   microsecond^2
+double const attogram_nanometersq_per_nanosecondsq_si =
+             attogram_si*pow(nanometer_si,2)/pow(nanosecond_si,2);
+                                            // [J] attogram*nanometer^2/
+                                            //   nanosecond^2
+
+/*----------------------
+   Velocity units
+------------------------ */
+double const angstrom_per_femtosecond_si =
+             angstrom_si/femtosecond_si;      // [m/s] Angstrom/femtosecond
+double const angstrom_per_picosecond_si =
+             angstrom_si/picosecond_si;       // [m/s] Angstrom/picosecond
+double const micrometer_per_microsecond_si =
+             micrometer_si/microsecond_si;    // [m/s] micrometer/microsecond
+double const nanometer_per_nanosecond_si =
+             nanometer_si/nanosecond_si;      // [m/s] nanometer/nanosecond
+double const centimeter_per_second_si =
+             centimeter_si;                  // [m/s] centimeter/second
+double const bohr_per_atu_electron_si =
+             bohr_si/atu_electron_si;        // [m/s] bohr/atu
+
+/*----------------------
+   Force units
+------------------------ */
+double const kcal_per_mole_angstrom_si =
+             kcal_per_mole_si/angstrom_si;       // [N] kcal/(mole*Angstrom)
+double const ev_per_angstrom_si =
+             ev_si/angstrom_si;                  // [N] eV/Angstrom
+double const dyne_si =
+             dyne_centimeter_si/centimeter_si;   // [N] dyne
+double const hartree_per_bohr_si =
+             hartree_si/bohr_si;                 // [N] hartree/bohr
+double const picogram_micrometer_per_microsecondsq_si =
+             picogram_si*micrometer_si/pow(microsecond_si,2);
+                                                 // [N] picogram*micrometer/
+                                                 //   microsecond^2
+double const attogram_nanometer_per_nanosecondsq_si =
+             attogram_si*nanometer_si/pow(nanosecond_si,2);
+                                                 // [N] attogram*nanometer/
+                                                 //   nanosecond^2
+
+/*----------------------
+   Pressure units
+------------------------ */
+double const atmosphere_si = 101325.0; // [Pa] standard atmosphere (NIST value)
+double const bar_si = 1e5;             // [Pa] bar
+double const dyne_per_centimetersq_si =
+             dyne_centimeter_si/pow(centimeter_si,3);
+                                       // [Pa] dyne/centimeter^2
+double const picogram_per_micrometer_microsecondsq_si =
+             picogram_si/(micrometer_si*pow(microsecond_si,2));
+                                       // [Pa] picogram/(micrometer*
+                                       //   microsecond^2)
+double const attogram_per_nanometer_nanosecondsq_si =
+             attogram_si/(nanometer_si*pow(nanosecond_si,2));
+                                       // [Pa] attogram/(nanometer*nanosecond^2)
+
+/*----------------------
+   Viscosity units
+------------------------ */
+double const poise_si = 0.1;                  // [Pa*s] Poise
+double const amu_per_bohr_femtosecond_si =
+             amu_si/(bohr_si*femtosecond_si); // [Pa*s] amu/(bohr*femtosecond)
+double const picogram_per_micrometer_microsecond_si =
+             picogram_si/(micrometer_si*microsecond_si);
+                                              // [Pa*s] picogram/(micrometer*
+                                              //   microsecond)
+double const attogram_per_nanometer_nanosecond_si =
+             attogram_si/(nanometer_si*nanosecond_si);
+                                              // [Pa*s] attogram/(nanometer*
+                                              //   nanosecond)
+
+/*----------------------
+   Charge units
+------------------------ */
+double const echarge_si = e_si;                   // [C] electron charge unit
+double const statcoulomb_si = e_si/4.8032044e-10; // [C] Statcoulomb or esu
+                                                  //   (value from LAMMPS units
+                                                  //   documentation)
+double const picocoulomb_si = 1e-12;              // [C] picocoulomb
+
+/*----------------------
+   Dipole units
+------------------------ */
+double const electron_angstrom_si = echarge_si*angstrom_si;
+                                                 // [C*m] electron*angstrom
+double const statcoulomb_centimeter_si = statcoulomb_si*centimeter_si;
+                                                 // [C*m] statcoulomb*centimeter
+double const debye_si = 1e-18*statcoulomb_centimeter_si;
+                                                 // [C*m] Debye
+double const picocoulomb_micrometer_si = picocoulomb_si*micrometer_si;
+                                                 // [C*m] picocoulomb*micrometer
+double const electron_nanometer_si = echarge_si*nanometer_si;
+                                                 // [C*m] electron*nanometer
+
+/*----------------------
+   Electric field units
+------------------------ */
+double const volt_per_angstrom_si = 1.0/angstrom_si;// [V/m] volt/angstrom
+double const statvolt_per_centimeter_si =
+             erg_si/(statcoulomb_si*centimeter_si); // [V/m] statvolt/centimeter
+double const volt_per_centimeter_si =
+             1.0/centimeter_si;                     // [V/m] volt/centimeter
+double const volt_per_micrometer_si =
+             1.0/micrometer_si;                     // [V/m] volt/micrometer
+double const volt_per_nanometer_si =
+             1.0/nanometer_si;                      // [V/m] volt/nanometer
+
+// Define enumerations
+enum sys_type
+{
+   real      = 1,
+   metal     = 2,
+   si        = 3,
+   cgs       = 4,
+   electron  = 5,
+   micro     = 6,
+   nano      = 7
+};
+
+enum unit_type
+{
+    mass         = 1,
+    distance     = 2,
+    time         = 3,
+    energy       = 4,
+    velocity     = 5,
+    force        = 6,
+    torque       = 7,
+    temperature  = 8,
+    pressure     = 9,
+    viscosity    = 10,
+    charge       = 11,
+    dipole       = 12,
+    efield       = 13,
+    density      = 14
+};
+
+enum units
+{
+    // mass
+    gram_per_mole = 101,
+    kilogram      = 102,
+    gram          = 103,
+    amu           = 104,
+    picogram      = 105,
+    attogram      = 106,
+    // distance
+    angstrom    = 201,
+    meter       = 202,
+    centimeter  = 203,
+    bohr        = 204,
+    micrometer  = 205,
+    nanometer   = 206,
+    // time
+    femtosecond  = 301,
+    picosecond   = 302,
+    second       = 303,
+    microsecond  = 304,
+    nanosecond   = 305,
+    // energy
+    kcal_per_mole = 401,
+    ev            = 402,
+    joule         = 403,
+    erg           = 404,
+    hartree       = 405,
+    picogram_micrometersq_per_microsecondsq = 406,
+    attogram_nanometersq_per_nanosecondsq   = 407,
+    // velocity
+    angstrom_per_femtosecond   = 501,
+    angstrom_per_picosecond    = 502,
+    meter_per_second           = 503,
+    centimeter_per_second      = 504,
+    bohr_per_atu               = 505,
+    micrometer_per_microsecond = 506,
+    nanometer_per_nanosecond   = 507,
+    // force
+    kcal_per_mole_angstrom = 601,
+    ev_per_angstrom        = 602,
+    newton                 = 603,
+    dyne                   = 604,
+    hartree_per_bohr       = 605,
+    picogram_micrometer_per_microsecondsq = 606,
+    attogram_nanometer_per_nanosecondsq   = 607,
+    // torque
+    newton_meter    = 701,
+    dyne_centimeter = 702,
+    // temperature
+    kelvin         = 801,
+    // pressure
+    atmosphere = 901,
+    bar        = 902,
+    pascal     = 903,
+    dyne_per_centimetersq                 = 904,
+    picogram_per_micrometer_microsecondsq = 905,
+    attogram_per_nanometer_nanosecondsq   = 906,
+    // viscosity
+    poise                    = 1001,
+    pascal_second            = 1002,
+    amu_per_bohr_femtosecond = 1003, // electron system, not in docs, GUESSED
+    picogram_per_micrometer_microsecond = 1004,
+    attogram_per_nanometer_nanosecond   = 1005,
+    // charge
+    echarge     = 1101,
+    coulomb     = 1102,
+    statcoulomb = 1103,
+    picocoulomb = 1104,
+    // dipole
+    electron_angstrom      = 1201,
+    coulomb_meter          = 1202,
+    statcoulomb_centimeter = 1203,
+    debye                  = 1204,
+    picocoulomb_micrometer = 1205,
+    electron_nanometer     = 1206,
+    // electric field
+    volt_per_angstrom       = 1301,
+    volt_per_meter          = 1302,
+    statvolt_per_centimeter = 1303,
+    volt_per_centimeter     = 1304,
+    volt_per_micrometer     = 1305,
+    volt_per_nanometer      = 1306,
+    // density
+    gram_per_centimetercu     = 1401,
+    kilogram_per_metercu      = 1402,
+    amu_per_bohrcu            = 1403, // electron system, not in docs, GUESSED
+    picogram_per_micrometercu = 1404,
+    attogram_per_nanometercu  = 1405
+};
+
+// Define dictionaries
+map<string, sys_type> system_dic;
+map<string, unit_type> unit_dic;
+map<unit_type, units> units_real_dic;
+map<unit_type, units> units_metal_dic;
+map<unit_type, units> units_si_dic;
+map<unit_type, units> units_cgs_dic;
+map<unit_type, units> units_electron_dic;
+map<unit_type, units> units_micro_dic;
+map<unit_type, units> units_nano_dic;
+
+/* ---------------------------------------------------------------------- */
+
+void initialize_dictionaries()
+{
+  system_dic["real"]     = real;
+  system_dic["metal"]    = metal;
+  system_dic["si"]       = si;
+  system_dic["cgs"]      = cgs;
+  system_dic["electron"] = electron;
+  system_dic["micro"]    = micro;
+  system_dic["nano"]     = nano;
+
+  unit_dic["mass"]       = mass;
+  unit_dic["distance"]   = distance;
+  unit_dic["time"]       = time;
+  unit_dic["energy"]     = energy;
+  unit_dic["velocity"]   = velocity;
+  unit_dic["force"]      = force;
+  unit_dic["torque"]     = torque;
+  unit_dic["temperature"]= temperature;
+  unit_dic["pressure"]   = pressure;
+  unit_dic["viscosity"]  = viscosity;
+  unit_dic["charge"]     = charge;
+  unit_dic["dipole"]     = dipole;
+  unit_dic["efield"]     = efield;
+  unit_dic["density"]    = density;
+
+  units_real_dic[mass]       = gram_per_mole;
+  units_real_dic[distance]   = angstrom;
+  units_real_dic[time]       = femtosecond;
+  units_real_dic[energy]     = kcal_per_mole;
+  units_real_dic[velocity]   = angstrom_per_femtosecond;
+  units_real_dic[force]      = kcal_per_mole_angstrom;
+  units_real_dic[torque]     = kcal_per_mole;
+  units_real_dic[temperature]= kelvin;
+  units_real_dic[pressure]   = atmosphere;
+  units_real_dic[viscosity]  = poise;
+  units_real_dic[charge]     = echarge;
+  units_real_dic[dipole]     = electron_angstrom;
+  units_real_dic[efield]     = volt_per_angstrom;
+  units_real_dic[density]    = gram_per_centimetercu;
+
+  units_metal_dic[mass]       = gram_per_mole;
+  units_metal_dic[distance]   = angstrom;
+  units_metal_dic[time]       = picosecond;
+  units_metal_dic[energy]     = ev;
+  units_metal_dic[velocity]   = angstrom_per_picosecond;
+  units_metal_dic[force]      = ev_per_angstrom;
+  units_metal_dic[torque]     = ev;
+  units_metal_dic[temperature]= kelvin;
+  units_metal_dic[pressure]   = bar;
+  units_metal_dic[viscosity]  = poise;
+  units_metal_dic[charge]     = echarge;
+  units_metal_dic[dipole]     = electron_angstrom;
+  units_metal_dic[efield]     = volt_per_angstrom;
+  units_metal_dic[density]    = gram_per_centimetercu;
+
+  units_si_dic[mass]       = kilogram;
+  units_si_dic[distance]   = meter;
+  units_si_dic[time]       = second;
+  units_si_dic[energy]     = joule;
+  units_si_dic[velocity]   = meter_per_second;
+  units_si_dic[force]      = newton;
+  units_si_dic[torque]     = newton_meter;
+  units_si_dic[temperature]= kelvin;
+  units_si_dic[pressure]   = pascal;
+  units_si_dic[viscosity]  = pascal_second;
+  units_si_dic[charge]     = coulomb;
+  units_si_dic[dipole]     = coulomb_meter;
+  units_si_dic[efield]     = volt_per_meter;
+  units_si_dic[density]    = kilogram_per_metercu;
+
+  units_cgs_dic[mass]       = gram;
+  units_cgs_dic[distance]   = centimeter;
+  units_cgs_dic[time]       = second;
+  units_cgs_dic[energy]     = erg;
+  units_cgs_dic[velocity]   = centimeter_per_second;
+  units_cgs_dic[force]      = dyne;
+  units_cgs_dic[torque]     = dyne_centimeter;
+  units_cgs_dic[temperature]= kelvin;
+  units_cgs_dic[pressure]   = dyne_per_centimetersq;
+  units_cgs_dic[viscosity]  = poise;
+  units_cgs_dic[charge]     = statcoulomb;
+  units_cgs_dic[dipole]     = statcoulomb_centimeter;
+  units_cgs_dic[efield]     = statvolt_per_centimeter;
+  units_cgs_dic[density]    = gram_per_centimetercu;
+
+  units_electron_dic[mass]       = amu;
+  units_electron_dic[distance]   = bohr;
+  units_electron_dic[time]       = femtosecond;
+  units_electron_dic[energy]     = hartree;
+  units_electron_dic[velocity]   = bohr_per_atu;
+  units_electron_dic[force]      = hartree_per_bohr;
+  units_electron_dic[torque]     = hartree;              // unknown, GUESSED
+  units_electron_dic[temperature]= kelvin;
+  units_electron_dic[pressure]   = pascal;
+  units_electron_dic[viscosity]  = pascal_second;        // unknown, GUESSED
+  units_electron_dic[charge]     = echarge;
+  units_electron_dic[dipole]     = debye;
+  units_electron_dic[efield]     = volt_per_centimeter;
+  units_electron_dic[density]    = amu_per_bohrcu;       // unknown, GUESSED
+
+  units_micro_dic[mass]       = picogram;
+  units_micro_dic[distance]   = micrometer;
+  units_micro_dic[time]       = microsecond;
+  units_micro_dic[energy]     = picogram_micrometersq_per_microsecondsq;
+  units_micro_dic[velocity]   = micrometer_per_microsecond;
+  units_micro_dic[force]      = picogram_micrometer_per_microsecondsq;
+  units_micro_dic[torque]     = picogram_micrometersq_per_microsecondsq;
+  units_micro_dic[temperature]= kelvin;
+  units_micro_dic[pressure]   = picogram_per_micrometer_microsecondsq;
+  units_micro_dic[viscosity]  = picogram_per_micrometer_microsecond;
+  units_micro_dic[charge]     = picocoulomb;
+  units_micro_dic[dipole]     = picocoulomb_micrometer;
+  units_micro_dic[efield]     = volt_per_micrometer;
+  units_micro_dic[density]    = picogram_per_micrometercu;
+
+  units_nano_dic[mass]       = attogram;
+  units_nano_dic[distance]   = nanometer;
+  units_nano_dic[time]       = nanosecond;
+  units_nano_dic[energy]     = attogram_nanometersq_per_nanosecondsq;
+  units_nano_dic[velocity]   = nanometer_per_nanosecond;
+  units_nano_dic[force]      = attogram_nanometer_per_nanosecondsq;
+  units_nano_dic[torque]     = attogram_nanometersq_per_nanosecondsq;
+  units_nano_dic[temperature]= kelvin;
+  units_nano_dic[pressure]   = attogram_per_nanometer_nanosecondsq;
+  units_nano_dic[viscosity]  = attogram_per_nanometer_nanosecond;
+  units_nano_dic[charge]     = echarge;
+  units_nano_dic[dipole]     = electron_nanometer;
+  units_nano_dic[efield]     = volt_per_nanometer;
+  units_nano_dic[density]    = attogram_per_nanometercu;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Get the enumeration for the unit of type `unit_type_enum`
+// for LAMMPS system `system_enum`.
+units get_lammps_system_unit(sys_type system_enum, unit_type unit_type_enum)
+{
+  switch(system_enum) {
+    case real :
+      return units_real_dic[unit_type_enum];
+    case metal :
+      return units_metal_dic[unit_type_enum];
+    case si :
+      return units_si_dic[unit_type_enum];
+    case cgs :
+      return units_cgs_dic[unit_type_enum];
+    case electron :
+      return units_electron_dic[unit_type_enum];
+    case micro :
+      return units_micro_dic[unit_type_enum];
+    case nano :
+    default :    // This is here to a prevent a compiler warning
+      return units_nano_dic[unit_type_enum];
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Mass conversion
+double get_mass_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[kilogram][kilogram]           = 1.0;
+  conv[kilogram][gram_per_mole]      = 1.0/gram_per_mole_si;
+  conv[kilogram][gram]               = 1.0/gram_si;
+  conv[kilogram][amu]                = 1.0/amu_si;
+  conv[kilogram][picogram]           = 1.0/picogram_si;
+  conv[kilogram][attogram]           = 1.0/attogram_si;
+
+  to_si = 1.0/conv[kilogram][gram_per_mole];
+  conv[gram_per_mole][kilogram]      = to_si*conv[kilogram][kilogram];
+  conv[gram_per_mole][gram_per_mole] = 1.0;
+  conv[gram_per_mole][gram]          = to_si*conv[kilogram][gram];
+  conv[gram_per_mole][amu]           = to_si*conv[kilogram][amu];
+  conv[gram_per_mole][picogram]      = to_si*conv[kilogram][picogram];
+  conv[gram_per_mole][attogram]      = to_si*conv[kilogram][attogram];
+
+  to_si = 1.0/conv[kilogram][gram];
+  conv[gram][kilogram]               = to_si*conv[kilogram][kilogram];
+  conv[gram][gram_per_mole]          = to_si*conv[kilogram][gram_per_mole];
+  conv[gram][gram]                   = 1.0;
+  conv[gram][amu]                    = to_si*conv[kilogram][amu];
+  conv[gram][picogram]               = to_si*conv[kilogram][picogram];
+  conv[gram][attogram]               = to_si*conv[kilogram][attogram];
+
+  to_si = 1.0/conv[kilogram][amu];
+  conv[amu][kilogram]                = to_si*conv[kilogram][kilogram];
+  conv[amu][gram_per_mole]           = to_si*conv[kilogram][gram_per_mole];
+  conv[amu][gram]                    = to_si*conv[kilogram][gram];
+  conv[amu][amu]                     = 1.0;
+  conv[amu][picogram]                = to_si*conv[kilogram][picogram];
+  conv[amu][attogram]                = to_si*conv[kilogram][attogram];
+
+  to_si = 1.0/conv[kilogram][picogram];
+  conv[picogram][kilogram]           = to_si*conv[kilogram][kilogram];
+  conv[picogram][gram_per_mole]      = to_si*conv[kilogram][gram_per_mole];
+  conv[picogram][gram]               = to_si*conv[kilogram][gram];
+  conv[picogram][amu]                = to_si*conv[kilogram][amu];
+  conv[picogram][picogram]           = 1.0;
+  conv[picogram][attogram]           = to_si*conv[kilogram][attogram];
+
+  to_si = 1.0/conv[kilogram][attogram];
+  conv[attogram][kilogram]           = to_si*conv[kilogram][kilogram];
+  conv[attogram][gram_per_mole]      = to_si*conv[kilogram][gram_per_mole];
+  conv[attogram][gram]               = to_si*conv[kilogram][gram];
+  conv[attogram][amu]                = to_si*conv[kilogram][amu];
+  conv[attogram][picogram]           = to_si*conv[kilogram][picogram];
+  conv[attogram][attogram]           = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Distance conversion
+double get_distance_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[meter][meter]           = 1.0;
+  conv[meter][angstrom]        = 1.0/angstrom_si;
+  conv[meter][centimeter]      = 1.0/centimeter_si;
+  conv[meter][bohr]            = 1.0/bohr_si;
+  conv[meter][micrometer]      = 1.0/micrometer_si;
+  conv[meter][nanometer]       = 1.0/nanometer_si;
+
+  to_si = 1.0/conv[meter][angstrom];
+  conv[angstrom][meter]        = to_si*conv[meter][meter];
+  conv[angstrom][angstrom]     = 1.0;
+  conv[angstrom][centimeter]   = to_si*conv[meter][centimeter];
+  conv[angstrom][bohr]         = to_si*conv[meter][bohr];
+  conv[angstrom][micrometer]   = to_si*conv[meter][micrometer];
+  conv[angstrom][nanometer]    = to_si*conv[meter][nanometer];
+
+  to_si = 1.0/conv[meter][centimeter];
+  conv[centimeter][meter]      = to_si*conv[meter][meter];
+  conv[centimeter][angstrom]   = to_si*conv[meter][angstrom];
+  conv[centimeter][centimeter] = 1.0;
+  conv[centimeter][bohr]       = to_si*conv[meter][bohr];
+  conv[centimeter][micrometer] = to_si*conv[meter][micrometer];
+  conv[centimeter][nanometer]  = to_si*conv[meter][nanometer];
+
+  to_si = 1.0/conv[meter][bohr];
+  conv[bohr][meter]            = to_si*conv[meter][meter];
+  conv[bohr][angstrom]         = to_si*conv[meter][angstrom];
+  conv[bohr][centimeter]       = to_si*conv[meter][centimeter];
+  conv[bohr][bohr]             = 1.0;
+  conv[bohr][micrometer]       = to_si*conv[meter][micrometer];
+  conv[bohr][nanometer]        = to_si*conv[meter][nanometer];
+
+  to_si = 1.0/conv[meter][micrometer];
+  conv[micrometer][meter]      = to_si*conv[meter][meter];
+  conv[micrometer][angstrom]   = to_si*conv[meter][angstrom];
+  conv[micrometer][centimeter] = to_si*conv[meter][centimeter];
+  conv[micrometer][bohr]       = to_si*conv[meter][bohr];
+  conv[micrometer][micrometer] = 1.0;
+  conv[micrometer][nanometer]  = to_si*conv[meter][nanometer];
+
+  to_si = 1.0/conv[meter][nanometer];
+  conv[nanometer][meter]       = to_si*conv[meter][meter];
+  conv[nanometer][angstrom]    = to_si*conv[meter][angstrom];
+  conv[nanometer][centimeter]  = to_si*conv[meter][centimeter];
+  conv[nanometer][bohr]        = to_si*conv[meter][bohr];
+  conv[nanometer][micrometer]  = to_si*conv[meter][micrometer];
+  conv[nanometer][nanometer]   = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Time conversion
+double get_time_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[second][second]           = 1.0;
+  conv[second][femtosecond]      = 1.0/femtosecond_si;
+  conv[second][picosecond]       = 1.0/picosecond_si;
+  conv[second][microsecond]      = 1.0/microsecond_si;
+  conv[second][nanosecond]       = 1.0/nanosecond_si;
+
+  to_si = 1.0/conv[second][femtosecond];
+  conv[femtosecond][second]      = to_si*conv[second][second];
+  conv[femtosecond][femtosecond] = 1.0;
+  conv[femtosecond][picosecond]  = to_si*conv[second][picosecond];
+  conv[femtosecond][microsecond] = to_si*conv[second][microsecond];
+  conv[femtosecond][nanosecond]  = to_si*conv[second][nanosecond];
+
+  to_si = 1.0/conv[second][picosecond];
+  conv[picosecond][second]       = to_si*conv[second][second];
+  conv[picosecond][femtosecond]  = to_si*conv[second][femtosecond];
+  conv[picosecond][picosecond]   = 1.0;
+  conv[picosecond][microsecond]  = to_si*conv[second][microsecond];
+  conv[picosecond][nanosecond]   = to_si*conv[second][nanosecond];
+
+  to_si = 1.0/conv[second][microsecond];
+  conv[microsecond][second]      = to_si*conv[second][second];
+  conv[microsecond][femtosecond] = to_si*conv[second][femtosecond];
+  conv[microsecond][picosecond]  = to_si*conv[second][picosecond];
+  conv[microsecond][microsecond] = 1.0;
+  conv[microsecond][nanosecond]  = to_si*conv[second][nanosecond];
+
+  to_si = 1.0/conv[second][nanosecond];
+  conv[nanosecond][second]       = to_si*conv[second][second];
+  conv[nanosecond][femtosecond]  = to_si*conv[second][femtosecond];
+  conv[nanosecond][picosecond]   = to_si*conv[second][picosecond];
+  conv[nanosecond][microsecond]  = to_si*conv[second][microsecond];
+  conv[nanosecond][nanosecond]   = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Energy conversion
+double get_energy_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[joule][joule]                                                                     = 1.0;
+  conv[joule][kcal_per_mole]                                                             = 1.0/kcal_per_mole_si;
+  conv[joule][ev]                                                                        = 1.0/ev_si;
+  conv[joule][erg]                                                                       = 1.0/erg_si;
+  conv[joule][hartree]                                                                   = 1.0/hartree_si;
+  conv[joule][picogram_micrometersq_per_microsecondsq]                                   = 1.0/picogram_micrometersq_per_microsecondsq_si;
+  conv[joule][attogram_nanometersq_per_nanosecondsq]                                     = 1.0/attogram_nanometersq_per_nanosecondsq_si;
+
+  to_si = 1.0/conv[joule][kcal_per_mole];
+  conv[kcal_per_mole][joule]                                                             = to_si*conv[joule][joule];
+  conv[kcal_per_mole][kcal_per_mole]                                                     = 1.0;
+  conv[kcal_per_mole][ev]                                                                = to_si*conv[joule][ev];
+  conv[kcal_per_mole][erg]                                                               = to_si*conv[joule][erg];
+  conv[kcal_per_mole][hartree]                                                           = to_si*conv[joule][hartree];
+  conv[kcal_per_mole][picogram_micrometersq_per_microsecondsq]                           = to_si*conv[joule][picogram_micrometersq_per_microsecondsq];
+  conv[kcal_per_mole][attogram_nanometersq_per_nanosecondsq]                             = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq];
+
+  to_si = 1.0/conv[joule][ev];
+  conv[ev][joule]                                                                        = to_si*conv[joule][joule];
+  conv[ev][kcal_per_mole]                                                                = to_si*conv[joule][kcal_per_mole];
+  conv[ev][ev]                                                                           = 1.0;
+  conv[ev][erg]                                                                          = to_si*conv[joule][erg];
+  conv[ev][hartree]                                                                      = to_si*conv[joule][hartree];
+  conv[ev][picogram_micrometersq_per_microsecondsq]                                      = to_si*conv[joule][picogram_micrometersq_per_microsecondsq];
+  conv[ev][attogram_nanometersq_per_nanosecondsq]                                        = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq];
+
+  to_si = 1.0/conv[joule][erg];
+  conv[erg][joule]                                                                       = to_si*conv[joule][joule];
+  conv[erg][kcal_per_mole]                                                               = to_si*conv[joule][kcal_per_mole];
+  conv[erg][ev]                                                                          = to_si*conv[joule][ev];
+  conv[erg][erg]                                                                         = 1.0;
+  conv[erg][hartree]                                                                     = to_si*conv[joule][hartree];
+  conv[erg][picogram_micrometersq_per_microsecondsq]                                     = to_si*conv[joule][picogram_micrometersq_per_microsecondsq];
+  conv[erg][attogram_nanometersq_per_nanosecondsq]                                       = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq];
+
+  to_si = 1.0/conv[joule][hartree];
+  conv[hartree][joule]                                                                   = to_si*conv[joule][joule];
+  conv[hartree][kcal_per_mole]                                                           = to_si*conv[joule][kcal_per_mole];
+  conv[hartree][ev]                                                                      = to_si*conv[joule][ev];
+  conv[hartree][erg]                                                                     = to_si*conv[joule][erg];
+  conv[hartree][hartree]                                                                 = 1.0;
+  conv[hartree][picogram_micrometersq_per_microsecondsq]                                 = to_si*conv[joule][picogram_micrometersq_per_microsecondsq];
+  conv[hartree][attogram_nanometersq_per_nanosecondsq]                                   = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq];
+
+  to_si = 1.0/conv[joule][picogram_micrometersq_per_microsecondsq];
+  conv[picogram_micrometersq_per_microsecondsq][joule]                                   = to_si*conv[joule][joule];
+  conv[picogram_micrometersq_per_microsecondsq][kcal_per_mole]                           = to_si*conv[joule][kcal_per_mole];
+  conv[picogram_micrometersq_per_microsecondsq][ev]                                      = to_si*conv[joule][ev];
+  conv[picogram_micrometersq_per_microsecondsq][erg]                                     = to_si*conv[joule][erg];
+  conv[picogram_micrometersq_per_microsecondsq][hartree]                                 = to_si*conv[joule][hartree];
+  conv[picogram_micrometersq_per_microsecondsq][picogram_micrometersq_per_microsecondsq] = 1.0;
+  conv[picogram_micrometersq_per_microsecondsq][attogram_nanometersq_per_nanosecondsq]   = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq];
+
+  to_si = 1.0/conv[joule][attogram_nanometersq_per_nanosecondsq];
+  conv[attogram_nanometersq_per_nanosecondsq][joule]                                     = to_si*conv[joule][joule];
+  conv[attogram_nanometersq_per_nanosecondsq][kcal_per_mole]                             = to_si*conv[joule][kcal_per_mole];
+  conv[attogram_nanometersq_per_nanosecondsq][ev]                                        = to_si*conv[joule][ev];
+  conv[attogram_nanometersq_per_nanosecondsq][erg]                                       = to_si*conv[joule][erg];
+  conv[attogram_nanometersq_per_nanosecondsq][hartree]                                   = to_si*conv[joule][hartree];
+  conv[attogram_nanometersq_per_nanosecondsq][picogram_micrometersq_per_microsecondsq]   = to_si*conv[joule][picogram_micrometersq_per_microsecondsq];
+  conv[attogram_nanometersq_per_nanosecondsq][attogram_nanometersq_per_nanosecondsq]     = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Velocity conversion
+double get_velocity_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[meter_per_second][meter_per_second]                     = 1.0;
+  conv[meter_per_second][angstrom_per_femtosecond]             = 1.0/angstrom_per_femtosecond_si;
+  conv[meter_per_second][angstrom_per_picosecond]              = 1.0/angstrom_per_picosecond_si;
+  conv[meter_per_second][centimeter_per_second]                = 1.0/centimeter_per_second_si;
+  conv[meter_per_second][bohr_per_atu]                         = 1.0/bohr_per_atu_electron_si;
+  conv[meter_per_second][micrometer_per_microsecond]           = 1.0/micrometer_per_microsecond_si;
+  conv[meter_per_second][nanometer_per_nanosecond]             = 1.0/nanometer_per_nanosecond_si;
+
+  to_si = 1.0/conv[meter_per_second][angstrom_per_femtosecond];
+  conv[angstrom_per_femtosecond][meter_per_second]             = to_si*conv[meter_per_second][meter_per_second];
+  conv[angstrom_per_femtosecond][angstrom_per_femtosecond]     = 1.0;
+  conv[angstrom_per_femtosecond][angstrom_per_picosecond]      = to_si*conv[meter_per_second][angstrom_per_picosecond];
+  conv[angstrom_per_femtosecond][centimeter_per_second]        = to_si*conv[meter_per_second][centimeter_per_second];
+  conv[angstrom_per_femtosecond][bohr_per_atu]                 = to_si*conv[meter_per_second][bohr_per_atu];
+  conv[angstrom_per_femtosecond][micrometer_per_microsecond]   = to_si*conv[meter_per_second][micrometer_per_microsecond];
+  conv[angstrom_per_femtosecond][nanometer_per_nanosecond]     = to_si*conv[meter_per_second][nanometer_per_nanosecond];
+
+  to_si = 1.0/conv[meter_per_second][angstrom_per_picosecond];
+  conv[angstrom_per_picosecond][meter_per_second]              = to_si*conv[meter_per_second][meter_per_second];
+  conv[angstrom_per_picosecond][angstrom_per_femtosecond]      = to_si*conv[meter_per_second][angstrom_per_femtosecond];
+  conv[angstrom_per_picosecond][angstrom_per_picosecond]       = 1.0;
+  conv[angstrom_per_picosecond][centimeter_per_second]         = to_si*conv[meter_per_second][centimeter_per_second];
+  conv[angstrom_per_picosecond][bohr_per_atu]                  = to_si*conv[meter_per_second][bohr_per_atu];
+  conv[angstrom_per_picosecond][micrometer_per_microsecond]    = to_si*conv[meter_per_second][micrometer_per_microsecond];
+  conv[angstrom_per_picosecond][nanometer_per_nanosecond]      = to_si*conv[meter_per_second][nanometer_per_nanosecond];
+
+  to_si = 1.0/conv[meter_per_second][centimeter_per_second];
+  conv[centimeter_per_second][meter_per_second]                = to_si*conv[meter_per_second][meter_per_second];
+  conv[centimeter_per_second][angstrom_per_femtosecond]        = to_si*conv[meter_per_second][angstrom_per_femtosecond];
+  conv[centimeter_per_second][angstrom_per_picosecond]         = to_si*conv[meter_per_second][angstrom_per_picosecond];
+  conv[centimeter_per_second][centimeter_per_second]           = 1.0;
+  conv[centimeter_per_second][bohr_per_atu]                    = to_si*conv[meter_per_second][bohr_per_atu];
+  conv[centimeter_per_second][micrometer_per_microsecond]      = to_si*conv[meter_per_second][micrometer_per_microsecond];
+  conv[centimeter_per_second][nanometer_per_nanosecond]        = to_si*conv[meter_per_second][nanometer_per_nanosecond];
+
+  to_si = 1.0/conv[meter_per_second][bohr_per_atu];
+  conv[bohr_per_atu][meter_per_second]                         = to_si*conv[meter_per_second][meter_per_second];
+  conv[bohr_per_atu][angstrom_per_femtosecond]                 = to_si*conv[meter_per_second][angstrom_per_femtosecond];
+  conv[bohr_per_atu][angstrom_per_picosecond]                  = to_si*conv[meter_per_second][angstrom_per_picosecond];
+  conv[bohr_per_atu][centimeter_per_second]                    = to_si*conv[meter_per_second][centimeter_per_second];
+  conv[bohr_per_atu][bohr_per_atu]                             = 1.0;
+  conv[bohr_per_atu][micrometer_per_microsecond]               = to_si*conv[meter_per_second][micrometer_per_microsecond];
+  conv[bohr_per_atu][nanometer_per_nanosecond]                 = to_si*conv[meter_per_second][nanometer_per_nanosecond];
+
+  to_si = 1.0/conv[meter_per_second][micrometer_per_microsecond];
+  conv[micrometer_per_microsecond][meter_per_second]           = to_si*conv[meter_per_second][meter_per_second];
+  conv[micrometer_per_microsecond][angstrom_per_femtosecond]   = to_si*conv[meter_per_second][angstrom_per_femtosecond];
+  conv[micrometer_per_microsecond][angstrom_per_picosecond]    = to_si*conv[meter_per_second][angstrom_per_picosecond];
+  conv[micrometer_per_microsecond][centimeter_per_second]      = to_si*conv[meter_per_second][centimeter_per_second];
+  conv[micrometer_per_microsecond][bohr_per_atu]               = to_si*conv[meter_per_second][bohr_per_atu];
+  conv[micrometer_per_microsecond][micrometer_per_microsecond] = 1.0;
+  conv[micrometer_per_microsecond][nanometer_per_nanosecond]   = to_si*conv[meter_per_second][nanometer_per_nanosecond];
+
+  to_si = 1.0/conv[meter_per_second][nanometer_per_nanosecond];
+  conv[nanometer_per_nanosecond][meter_per_second]             = to_si*conv[meter_per_second][meter_per_second];
+  conv[nanometer_per_nanosecond][angstrom_per_femtosecond]     = to_si*conv[meter_per_second][angstrom_per_femtosecond];
+  conv[nanometer_per_nanosecond][angstrom_per_picosecond]      = to_si*conv[meter_per_second][angstrom_per_picosecond];
+  conv[nanometer_per_nanosecond][centimeter_per_second]        = to_si*conv[meter_per_second][centimeter_per_second];
+  conv[nanometer_per_nanosecond][bohr_per_atu]                 = to_si*conv[meter_per_second][bohr_per_atu];
+  conv[nanometer_per_nanosecond][micrometer_per_microsecond]   = to_si*conv[meter_per_second][micrometer_per_microsecond];
+  conv[nanometer_per_nanosecond][nanometer_per_nanosecond]     = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Force conversion
+double get_force_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[newton][newton]                                                               = 1.0;
+  conv[newton][kcal_per_mole_angstrom]                                               = 1.0/kcal_per_mole_angstrom_si;
+  conv[newton][ev_per_angstrom]                                                      = 1.0/ev_per_angstrom_si;
+  conv[newton][dyne]                                                                 = 1.0/dyne_si;
+  conv[newton][hartree_per_bohr]                                                     = 1.0/hartree_per_bohr_si;
+  conv[newton][picogram_micrometer_per_microsecondsq]                                = 1.0/picogram_micrometer_per_microsecondsq_si;
+  conv[newton][attogram_nanometer_per_nanosecondsq]                                  = 1.0/attogram_nanometer_per_nanosecondsq_si;
+
+  to_si = 1.0/conv[newton][kcal_per_mole_angstrom];
+  conv[kcal_per_mole_angstrom][newton]                                               = to_si*conv[newton][newton];
+  conv[kcal_per_mole_angstrom][kcal_per_mole_angstrom]                               = 1.0;
+  conv[kcal_per_mole_angstrom][ev_per_angstrom]                                      = to_si*conv[newton][ev_per_angstrom];
+  conv[kcal_per_mole_angstrom][dyne]                                                 = to_si*conv[newton][dyne];
+  conv[kcal_per_mole_angstrom][hartree_per_bohr]                                     = to_si*conv[newton][hartree_per_bohr];
+  conv[kcal_per_mole_angstrom][picogram_micrometer_per_microsecondsq]                = to_si*conv[newton][picogram_micrometer_per_microsecondsq];
+  conv[kcal_per_mole_angstrom][attogram_nanometer_per_nanosecondsq]                  = to_si*conv[newton][attogram_nanometer_per_nanosecondsq];
+
+  to_si = 1.0/conv[newton][ev_per_angstrom];
+  conv[ev_per_angstrom][newton]                                                      = to_si*conv[newton][newton];
+  conv[ev_per_angstrom][kcal_per_mole_angstrom]                                      = to_si*conv[newton][kcal_per_mole_angstrom];
+  conv[ev_per_angstrom][ev_per_angstrom]                                             = 1.0;
+  conv[ev_per_angstrom][dyne]                                                        = to_si*conv[newton][dyne];
+  conv[ev_per_angstrom][hartree_per_bohr]                                            = to_si*conv[newton][hartree_per_bohr];
+  conv[ev_per_angstrom][picogram_micrometer_per_microsecondsq]                       = to_si*conv[newton][picogram_micrometer_per_microsecondsq];
+  conv[ev_per_angstrom][attogram_nanometer_per_nanosecondsq]                         = to_si*conv[newton][attogram_nanometer_per_nanosecondsq];
+
+  to_si = 1.0/conv[newton][dyne];
+  conv[dyne][newton]                                                                 = to_si*conv[newton][newton];
+  conv[dyne][kcal_per_mole_angstrom]                                                 = to_si*conv[newton][kcal_per_mole_angstrom];
+  conv[dyne][ev_per_angstrom]                                                        = to_si*conv[newton][ev_per_angstrom];
+  conv[dyne][dyne]                                                                   = 1.0;
+  conv[dyne][hartree_per_bohr]                                                       = to_si*conv[newton][hartree_per_bohr];
+  conv[dyne][picogram_micrometer_per_microsecondsq]                                  = to_si*conv[newton][picogram_micrometer_per_microsecondsq];
+  conv[dyne][attogram_nanometer_per_nanosecondsq]                                    = to_si*conv[newton][attogram_nanometer_per_nanosecondsq];
+
+  to_si = 1.0/conv[newton][hartree_per_bohr];
+  conv[hartree_per_bohr][newton]                                                     = to_si*conv[newton][newton];
+  conv[hartree_per_bohr][kcal_per_mole_angstrom]                                     = to_si*conv[newton][kcal_per_mole_angstrom];
+  conv[hartree_per_bohr][ev_per_angstrom]                                            = to_si*conv[newton][ev_per_angstrom];
+  conv[hartree_per_bohr][dyne]                                                       = to_si*conv[newton][dyne];
+  conv[hartree_per_bohr][hartree_per_bohr]                                           = 1.0;
+  conv[hartree_per_bohr][picogram_micrometer_per_microsecondsq]                      = to_si*conv[newton][picogram_micrometer_per_microsecondsq];
+  conv[hartree_per_bohr][attogram_nanometer_per_nanosecondsq]                        = to_si*conv[newton][attogram_nanometer_per_nanosecondsq];
+
+  to_si = 1.0/conv[newton][picogram_micrometer_per_microsecondsq];
+  conv[picogram_micrometer_per_microsecondsq][newton]                                = to_si*conv[newton][newton];
+  conv[picogram_micrometer_per_microsecondsq][kcal_per_mole_angstrom]                = to_si*conv[newton][kcal_per_mole_angstrom];
+  conv[picogram_micrometer_per_microsecondsq][ev_per_angstrom]                       = to_si*conv[newton][ev_per_angstrom];
+  conv[picogram_micrometer_per_microsecondsq][dyne]                                  = to_si*conv[newton][dyne];
+  conv[picogram_micrometer_per_microsecondsq][hartree_per_bohr]                      = to_si*conv[newton][hartree_per_bohr];
+  conv[picogram_micrometer_per_microsecondsq][picogram_micrometer_per_microsecondsq] = 1.0;
+  conv[picogram_micrometer_per_microsecondsq][attogram_nanometer_per_nanosecondsq]   = to_si*conv[newton][attogram_nanometer_per_nanosecondsq];
+
+  to_si = 1.0/conv[newton][attogram_nanometer_per_nanosecondsq];
+  conv[attogram_nanometer_per_nanosecondsq][newton]                                  = to_si*conv[newton][newton];
+  conv[attogram_nanometer_per_nanosecondsq][kcal_per_mole_angstrom]                  = to_si*conv[newton][kcal_per_mole_angstrom];
+  conv[attogram_nanometer_per_nanosecondsq][ev_per_angstrom]                         = to_si*conv[newton][ev_per_angstrom];
+  conv[attogram_nanometer_per_nanosecondsq][dyne]                                    = to_si*conv[newton][dyne];
+  conv[attogram_nanometer_per_nanosecondsq][hartree_per_bohr]                        = to_si*conv[newton][hartree_per_bohr];
+  conv[attogram_nanometer_per_nanosecondsq][picogram_micrometer_per_microsecondsq]   = to_si*conv[newton][picogram_micrometer_per_microsecondsq];
+  conv[attogram_nanometer_per_nanosecondsq][attogram_nanometer_per_nanosecondsq]     = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Torque conversion
+double get_torque_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[newton_meter][newton_meter]                                                       = 1.0;
+  conv[newton_meter][kcal_per_mole]                                                      = 1.0/kcal_per_mole_si;
+  conv[newton_meter][ev]                                                                 = 1.0/ev_si;
+  conv[newton_meter][dyne_centimeter]                                                    = 1.0/dyne_centimeter_si;
+  conv[newton_meter][hartree]                                                            = 1.0/hartree_si;
+  conv[newton_meter][picogram_micrometersq_per_microsecondsq]                            = 1.0/picogram_micrometersq_per_microsecondsq_si;
+  conv[newton_meter][attogram_nanometersq_per_nanosecondsq]                              = 1.0/attogram_nanometersq_per_nanosecondsq_si;
+
+  to_si = 1.0/conv[newton_meter][kcal_per_mole];
+  conv[kcal_per_mole][newton_meter]                                                      = to_si*conv[newton_meter][newton_meter];
+  conv[kcal_per_mole][kcal_per_mole]                                                     = 1.0;
+  conv[kcal_per_mole][ev]                                                                = to_si*conv[newton_meter][ev];
+  conv[kcal_per_mole][dyne_centimeter]                                                   = to_si*conv[newton_meter][dyne_centimeter];
+  conv[kcal_per_mole][hartree]                                                           = to_si*conv[newton_meter][hartree];
+  conv[kcal_per_mole][picogram_micrometersq_per_microsecondsq]                           = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq];
+  conv[kcal_per_mole][attogram_nanometersq_per_nanosecondsq]                             = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq];
+
+  to_si = 1.0/conv[newton_meter][ev];
+  conv[ev][newton_meter]                                                                 = to_si*conv[newton_meter][newton_meter];
+  conv[ev][kcal_per_mole]                                                                = to_si*conv[newton_meter][kcal_per_mole];
+  conv[ev][ev]                                                                           = 1.0;
+  conv[ev][dyne_centimeter]                                                              = to_si*conv[newton_meter][dyne_centimeter];
+  conv[ev][hartree]                                                                      = to_si*conv[newton_meter][hartree];
+  conv[ev][picogram_micrometersq_per_microsecondsq]                                      = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq];
+  conv[ev][attogram_nanometersq_per_nanosecondsq]                                        = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq];
+
+  to_si = 1.0/conv[newton_meter][dyne_centimeter];
+  conv[dyne_centimeter][newton_meter]                                                    = to_si*conv[newton_meter][newton_meter];
+  conv[dyne_centimeter][kcal_per_mole]                                                   = to_si*conv[newton_meter][kcal_per_mole];
+  conv[dyne_centimeter][ev]                                                              = to_si*conv[newton_meter][ev];
+  conv[dyne_centimeter][dyne_centimeter]                                                 = 1.0;
+  conv[dyne_centimeter][hartree]                                                         = to_si*conv[newton_meter][hartree];
+  conv[dyne_centimeter][picogram_micrometersq_per_microsecondsq]                         = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq];
+  conv[dyne_centimeter][attogram_nanometersq_per_nanosecondsq]                           = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq];
+
+  to_si = 1.0/conv[newton_meter][hartree];
+  conv[hartree][newton_meter]                                                            = to_si*conv[newton_meter][newton_meter];
+  conv[hartree][kcal_per_mole]                                                           = to_si*conv[newton_meter][kcal_per_mole];
+  conv[hartree][ev]                                                                      = to_si*conv[newton_meter][ev];
+  conv[hartree][dyne_centimeter]                                                         = to_si*conv[newton_meter][dyne_centimeter];
+  conv[hartree][hartree]                                                                 = 1.0;
+  conv[hartree][picogram_micrometersq_per_microsecondsq]                                 = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq];
+  conv[hartree][attogram_nanometersq_per_nanosecondsq]                                   = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq];
+
+  to_si = 1.0/conv[newton_meter][picogram_micrometersq_per_microsecondsq];
+  conv[picogram_micrometersq_per_microsecondsq][newton_meter]                            = to_si*conv[newton_meter][newton_meter];
+  conv[picogram_micrometersq_per_microsecondsq][kcal_per_mole]                           = to_si*conv[newton_meter][kcal_per_mole];
+  conv[picogram_micrometersq_per_microsecondsq][ev]                                      = to_si*conv[newton_meter][ev];
+  conv[picogram_micrometersq_per_microsecondsq][dyne_centimeter]                         = to_si*conv[newton_meter][dyne_centimeter];
+  conv[picogram_micrometersq_per_microsecondsq][hartree]                                 = to_si*conv[newton_meter][hartree];
+  conv[picogram_micrometersq_per_microsecondsq][picogram_micrometersq_per_microsecondsq] = 1.0;
+  conv[picogram_micrometersq_per_microsecondsq][attogram_nanometersq_per_nanosecondsq]   = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq];
+
+  to_si = 1.0/conv[newton_meter][attogram_nanometersq_per_nanosecondsq];
+  conv[attogram_nanometersq_per_nanosecondsq][newton_meter]                              = to_si*conv[newton_meter][newton_meter];
+  conv[attogram_nanometersq_per_nanosecondsq][kcal_per_mole]                             = to_si*conv[newton_meter][kcal_per_mole];
+  conv[attogram_nanometersq_per_nanosecondsq][ev]                                        = to_si*conv[newton_meter][ev];
+  conv[attogram_nanometersq_per_nanosecondsq][dyne_centimeter]                           = to_si*conv[newton_meter][dyne_centimeter];
+  conv[attogram_nanometersq_per_nanosecondsq][hartree]                                   = to_si*conv[newton_meter][hartree];
+  conv[attogram_nanometersq_per_nanosecondsq][picogram_micrometersq_per_microsecondsq]   = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq];
+  conv[attogram_nanometersq_per_nanosecondsq][attogram_nanometersq_per_nanosecondsq]     = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Temperature conversion
+double get_temperature_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[kelvin][kelvin] = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Pressure conversion
+double get_pressure_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[pascal][pascal]                                                               = 1.0;
+  conv[pascal][atmosphere]                                                           = 1.0/atmosphere_si;
+  conv[pascal][bar]                                                                  = 1.0/bar_si;
+  conv[pascal][dyne_per_centimetersq]                                                = 1.0/dyne_per_centimetersq_si;
+  conv[pascal][picogram_per_micrometer_microsecondsq]                                = 1.0/picogram_per_micrometer_microsecondsq_si;
+  conv[pascal][attogram_per_nanometer_nanosecondsq]                                  = 1.0/attogram_per_nanometer_nanosecondsq_si;
+
+  to_si = 1.0/conv[pascal][atmosphere];
+  conv[atmosphere][pascal]                                                           = to_si*conv[pascal][pascal];
+  conv[atmosphere][atmosphere]                                                       = 1.0;
+  conv[atmosphere][bar]                                                              = to_si*conv[pascal][bar];
+  conv[atmosphere][dyne_per_centimetersq]                                            = to_si*conv[pascal][dyne_per_centimetersq];
+  conv[atmosphere][picogram_per_micrometer_microsecondsq]                            = to_si*conv[pascal][picogram_per_micrometer_microsecondsq];
+  conv[atmosphere][attogram_per_nanometer_nanosecondsq]                              = to_si*conv[pascal][attogram_per_nanometer_nanosecondsq];
+
+  to_si = 1.0/conv[pascal][bar];
+  conv[bar][pascal]                                                                  = to_si*conv[pascal][pascal];
+  conv[bar][atmosphere]                                                              = to_si*conv[pascal][atmosphere];
+  conv[bar][bar]                                                                     = 1.0;
+  conv[bar][dyne_per_centimetersq]                                                   = to_si*conv[pascal][dyne_per_centimetersq];
+  conv[bar][picogram_per_micrometer_microsecondsq]                                   = to_si*conv[pascal][picogram_per_micrometer_microsecondsq];
+  conv[bar][attogram_per_nanometer_nanosecondsq]                                     = to_si*conv[pascal][attogram_per_nanometer_nanosecondsq];
+
+  to_si = 1.0/conv[pascal][dyne_per_centimetersq];
+  conv[dyne_per_centimetersq][pascal]                                                = to_si*conv[pascal][pascal];
+  conv[dyne_per_centimetersq][atmosphere]                                            = to_si*conv[pascal][atmosphere];
+  conv[dyne_per_centimetersq][bar]                                                   = to_si*conv[pascal][bar];
+  conv[dyne_per_centimetersq][dyne_per_centimetersq]                                 = 1.0;
+  conv[dyne_per_centimetersq][picogram_per_micrometer_microsecondsq]                 = to_si*conv[pascal][picogram_per_micrometer_microsecondsq];
+  conv[dyne_per_centimetersq][attogram_per_nanometer_nanosecondsq]                   = to_si*conv[pascal][attogram_per_nanometer_nanosecondsq];
+
+  to_si = 1.0/conv[pascal][picogram_per_micrometer_microsecondsq];
+  conv[picogram_per_micrometer_microsecondsq][pascal]                                = to_si*conv[pascal][pascal];
+  conv[picogram_per_micrometer_microsecondsq][atmosphere]                            = to_si*conv[pascal][atmosphere];
+  conv[picogram_per_micrometer_microsecondsq][bar]                                   = to_si*conv[pascal][bar];
+  conv[picogram_per_micrometer_microsecondsq][dyne_per_centimetersq]                 = to_si*conv[pascal][dyne_per_centimetersq];
+  conv[picogram_per_micrometer_microsecondsq][picogram_per_micrometer_microsecondsq] = 1.0;
+  conv[picogram_per_micrometer_microsecondsq][attogram_per_nanometer_nanosecondsq]   = to_si*conv[pascal][attogram_per_nanometer_nanosecondsq];
+
+  to_si = 1.0/conv[pascal][attogram_per_nanometer_nanosecondsq];
+  conv[attogram_per_nanometer_nanosecondsq][pascal]                                  = to_si*conv[pascal][pascal];
+  conv[attogram_per_nanometer_nanosecondsq][atmosphere]                              = to_si*conv[pascal][atmosphere];
+  conv[attogram_per_nanometer_nanosecondsq][bar]                                     = to_si*conv[pascal][bar];
+  conv[attogram_per_nanometer_nanosecondsq][dyne_per_centimetersq]                   = to_si*conv[pascal][dyne_per_centimetersq];
+  conv[attogram_per_nanometer_nanosecondsq][picogram_per_micrometer_microsecondsq]   = to_si*conv[pascal][picogram_per_micrometer_microsecondsq];
+  conv[attogram_per_nanometer_nanosecondsq][attogram_per_nanometer_nanosecondsq]     = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Viscosity conversion
+double get_viscosity_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[pascal_second][pascal_second]                                             = 1.0;
+  conv[pascal_second][poise]                                                     = 1.0/poise_si;
+  conv[pascal_second][amu_per_bohr_femtosecond]                                  = 1.0/amu_per_bohr_femtosecond_si;
+  conv[pascal_second][picogram_per_micrometer_microsecond]                       = 1.0/picogram_per_micrometer_microsecond_si;
+  conv[pascal_second][attogram_per_nanometer_nanosecond]                         = 1.0/attogram_per_nanometer_nanosecond_si;
+
+  to_si = 1.0/conv[pascal_second][poise];
+  conv[poise][pascal_second]                                                     = to_si*conv[pascal_second][pascal_second];
+  conv[poise][poise]                                                             = 1.0;
+  conv[poise][amu_per_bohr_femtosecond]                                          = to_si*conv[pascal_second][amu_per_bohr_femtosecond];
+  conv[poise][picogram_per_micrometer_microsecond]                               = to_si*conv[pascal_second][picogram_per_micrometer_microsecond];
+  conv[poise][attogram_per_nanometer_nanosecond]                                 = to_si*conv[pascal_second][attogram_per_nanometer_nanosecond];
+
+  to_si = 1.0/conv[pascal_second][amu_per_bohr_femtosecond];
+  conv[amu_per_bohr_femtosecond][pascal_second]                                  = to_si*conv[pascal_second][pascal_second];
+  conv[amu_per_bohr_femtosecond][poise]                                          = to_si*conv[pascal_second][poise];
+  conv[amu_per_bohr_femtosecond][amu_per_bohr_femtosecond]                       = 1.0;
+  conv[amu_per_bohr_femtosecond][picogram_per_micrometer_microsecond]            = to_si*conv[pascal_second][picogram_per_micrometer_microsecond];
+  conv[amu_per_bohr_femtosecond][attogram_per_nanometer_nanosecond]              = to_si*conv[pascal_second][attogram_per_nanometer_nanosecond];
+
+  to_si = 1.0/conv[pascal_second][picogram_per_micrometer_microsecond];
+  conv[picogram_per_micrometer_microsecond][pascal_second]                       = to_si*conv[pascal_second][pascal_second];
+  conv[picogram_per_micrometer_microsecond][poise]                               = to_si*conv[pascal_second][poise];
+  conv[picogram_per_micrometer_microsecond][amu_per_bohr_femtosecond]            = to_si*conv[pascal_second][amu_per_bohr_femtosecond];
+  conv[picogram_per_micrometer_microsecond][picogram_per_micrometer_microsecond] = 1.0;
+  conv[picogram_per_micrometer_microsecond][attogram_per_nanometer_nanosecond]   = to_si*conv[pascal_second][attogram_per_nanometer_nanosecond];
+
+  to_si = 1.0/conv[pascal_second][attogram_per_nanometer_nanosecond];
+  conv[attogram_per_nanometer_nanosecond][pascal_second]                         = to_si*conv[pascal_second][pascal_second];
+  conv[attogram_per_nanometer_nanosecond][poise]                                 = to_si*conv[pascal_second][poise];
+  conv[attogram_per_nanometer_nanosecond][amu_per_bohr_femtosecond]              = to_si*conv[pascal_second][amu_per_bohr_femtosecond];
+  conv[attogram_per_nanometer_nanosecond][picogram_per_micrometer_microsecond]   = to_si*conv[pascal_second][picogram_per_micrometer_microsecond];
+  conv[attogram_per_nanometer_nanosecond][attogram_per_nanometer_nanosecond]     = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Charge conversion
+double get_charge_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[coulomb][coulomb]         = 1.0;
+  conv[coulomb][echarge]         = 1.0/echarge_si;
+  conv[coulomb][statcoulomb]     = 1.0/statcoulomb_si;
+  conv[coulomb][picocoulomb]     = 1.0/picocoulomb_si;
+
+  to_si = 1.0/conv[coulomb][echarge];
+  conv[echarge][coulomb]         = to_si*conv[coulomb][coulomb];
+  conv[echarge][echarge]         = 1.0;
+  conv[echarge][statcoulomb]     = to_si*conv[coulomb][statcoulomb];
+  conv[echarge][picocoulomb]     = to_si*conv[coulomb][picocoulomb];
+
+  to_si = 1.0/conv[coulomb][statcoulomb];
+  conv[statcoulomb][coulomb]     = to_si*conv[coulomb][coulomb];
+  conv[statcoulomb][echarge]     = to_si*conv[coulomb][echarge];
+  conv[statcoulomb][statcoulomb] = 1.0;
+  conv[statcoulomb][picocoulomb] = to_si*conv[coulomb][picocoulomb];
+
+  to_si = 1.0/conv[coulomb][picocoulomb];
+  conv[picocoulomb][coulomb]     = to_si*conv[coulomb][coulomb];
+  conv[picocoulomb][echarge]     = to_si*conv[coulomb][echarge];
+  conv[picocoulomb][statcoulomb] = to_si*conv[coulomb][statcoulomb];
+  conv[picocoulomb][picocoulomb] = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Dipole conversion
+double get_dipole_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[coulomb_meter][coulomb_meter]                   = 1.0;
+  conv[coulomb_meter][electron_angstrom]               = 1.0/electron_angstrom_si;
+  conv[coulomb_meter][statcoulomb_centimeter]          = 1.0/statcoulomb_centimeter_si;
+  conv[coulomb_meter][debye]                           = 1.0/debye_si;
+  conv[coulomb_meter][picocoulomb_micrometer]          = 1.0/picocoulomb_micrometer_si;
+  conv[coulomb_meter][electron_nanometer]              = 1.0/electron_nanometer_si;
+
+  to_si = 1.0/conv[coulomb_meter][electron_angstrom];
+  conv[electron_angstrom][coulomb_meter]               = to_si*conv[coulomb_meter][coulomb_meter];
+  conv[electron_angstrom][electron_angstrom]           = 1.0;
+  conv[electron_angstrom][statcoulomb_centimeter]      = to_si*conv[coulomb_meter][statcoulomb_centimeter];
+  conv[electron_angstrom][debye]                       = to_si*conv[coulomb_meter][debye];
+  conv[electron_angstrom][picocoulomb_micrometer]      = to_si*conv[coulomb_meter][picocoulomb_micrometer];
+  conv[electron_angstrom][electron_nanometer]          = to_si*conv[coulomb_meter][electron_nanometer];
+
+  to_si = 1.0/conv[coulomb_meter][statcoulomb_centimeter];
+  conv[statcoulomb_centimeter][coulomb_meter]          = to_si*conv[coulomb_meter][coulomb_meter];
+  conv[statcoulomb_centimeter][electron_angstrom]      = to_si*conv[coulomb_meter][electron_angstrom];
+  conv[statcoulomb_centimeter][statcoulomb_centimeter] = 1.0;
+  conv[statcoulomb_centimeter][debye]                  = to_si*conv[coulomb_meter][debye];
+  conv[statcoulomb_centimeter][picocoulomb_micrometer] = to_si*conv[coulomb_meter][picocoulomb_micrometer];
+  conv[statcoulomb_centimeter][electron_nanometer]     = to_si*conv[coulomb_meter][electron_nanometer];
+
+  to_si = 1.0/conv[coulomb_meter][debye];
+  conv[debye][coulomb_meter]                           = to_si*conv[coulomb_meter][coulomb_meter];
+  conv[debye][electron_angstrom]                       = to_si*conv[coulomb_meter][electron_angstrom];
+  conv[debye][statcoulomb_centimeter]                  = to_si*conv[coulomb_meter][statcoulomb_centimeter];
+  conv[debye][debye]                                   = 1.0;
+  conv[debye][picocoulomb_micrometer]                  = to_si*conv[coulomb_meter][picocoulomb_micrometer];
+  conv[debye][electron_nanometer]                      = to_si*conv[coulomb_meter][electron_nanometer];
+
+  to_si = 1.0/conv[coulomb_meter][picocoulomb_micrometer];
+  conv[picocoulomb_micrometer][coulomb_meter]          = to_si*conv[coulomb_meter][coulomb_meter];
+  conv[picocoulomb_micrometer][electron_angstrom]      = to_si*conv[coulomb_meter][electron_angstrom];
+  conv[picocoulomb_micrometer][statcoulomb_centimeter] = to_si*conv[coulomb_meter][statcoulomb_centimeter];
+  conv[picocoulomb_micrometer][debye]                  = to_si*conv[coulomb_meter][debye];
+  conv[picocoulomb_micrometer][picocoulomb_micrometer] = 1.0;
+  conv[picocoulomb_micrometer][electron_nanometer]     = to_si*conv[coulomb_meter][electron_nanometer];
+
+  to_si = 1.0/conv[coulomb_meter][electron_nanometer];
+  conv[electron_nanometer][coulomb_meter]              = to_si*conv[coulomb_meter][coulomb_meter];
+  conv[electron_nanometer][electron_angstrom]          = to_si*conv[coulomb_meter][electron_angstrom];
+  conv[electron_nanometer][statcoulomb_centimeter]     = to_si*conv[coulomb_meter][statcoulomb_centimeter];
+  conv[electron_nanometer][debye]                      = to_si*conv[coulomb_meter][debye];
+  conv[electron_nanometer][picocoulomb_micrometer]     = to_si*conv[coulomb_meter][picocoulomb_micrometer];
+  conv[electron_nanometer][electron_nanometer]         = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Electric field conversion
+double get_efield_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[volt_per_meter][volt_per_meter]                   = 1.0;
+  conv[volt_per_meter][volt_per_angstrom]                = 1.0/volt_per_angstrom_si;
+  conv[volt_per_meter][statvolt_per_centimeter]          = 1.0/statvolt_per_centimeter_si;
+  conv[volt_per_meter][volt_per_centimeter]              = 1.0/volt_per_centimeter_si;
+  conv[volt_per_meter][volt_per_micrometer]              = 1.0/volt_per_micrometer_si;
+  conv[volt_per_meter][volt_per_nanometer]               = 1.0/volt_per_nanometer_si;
+
+  to_si = 1.0/conv[volt_per_meter][volt_per_angstrom];
+  conv[volt_per_angstrom][volt_per_meter]                = to_si*conv[volt_per_meter][volt_per_meter];
+  conv[volt_per_angstrom][volt_per_angstrom]             = 1.0;
+  conv[volt_per_angstrom][statvolt_per_centimeter]       = to_si*conv[volt_per_meter][statvolt_per_centimeter];
+  conv[volt_per_angstrom][volt_per_centimeter]           = to_si*conv[volt_per_meter][volt_per_centimeter];
+  conv[volt_per_angstrom][volt_per_micrometer]           = to_si*conv[volt_per_meter][volt_per_micrometer];
+  conv[volt_per_angstrom][volt_per_nanometer]            = to_si*conv[volt_per_meter][volt_per_nanometer];
+
+  to_si = 1.0/conv[volt_per_meter][statvolt_per_centimeter];
+  conv[statvolt_per_centimeter][volt_per_meter]          = to_si*conv[volt_per_meter][volt_per_meter];
+  conv[statvolt_per_centimeter][volt_per_angstrom]       = to_si*conv[volt_per_meter][volt_per_angstrom];
+  conv[statvolt_per_centimeter][statvolt_per_centimeter] = 1.0;
+  conv[statvolt_per_centimeter][volt_per_centimeter]     = to_si*conv[volt_per_meter][volt_per_centimeter];
+  conv[statvolt_per_centimeter][volt_per_micrometer]     = to_si*conv[volt_per_meter][volt_per_micrometer];
+  conv[statvolt_per_centimeter][volt_per_nanometer]      = to_si*conv[volt_per_meter][volt_per_nanometer];
+
+  to_si = 1.0/conv[volt_per_meter][volt_per_centimeter];
+  conv[volt_per_centimeter][volt_per_meter]              = to_si*conv[volt_per_meter][volt_per_meter];
+  conv[volt_per_centimeter][volt_per_angstrom]           = to_si*conv[volt_per_meter][volt_per_angstrom];
+  conv[volt_per_centimeter][statvolt_per_centimeter]     = to_si*conv[volt_per_meter][statvolt_per_centimeter];
+  conv[volt_per_centimeter][volt_per_centimeter]         = 1.0;
+  conv[volt_per_centimeter][volt_per_micrometer]         = to_si*conv[volt_per_meter][volt_per_micrometer];
+  conv[volt_per_centimeter][volt_per_nanometer]          = to_si*conv[volt_per_meter][volt_per_nanometer];
+
+  to_si = 1.0/conv[volt_per_meter][volt_per_micrometer];
+  conv[volt_per_micrometer][volt_per_meter]              = to_si*conv[volt_per_meter][volt_per_meter];
+  conv[volt_per_micrometer][volt_per_angstrom]           = to_si*conv[volt_per_meter][volt_per_angstrom];
+  conv[volt_per_micrometer][statvolt_per_centimeter]     = to_si*conv[volt_per_meter][statvolt_per_centimeter];
+  conv[volt_per_micrometer][volt_per_centimeter]         = to_si*conv[volt_per_meter][volt_per_centimeter];
+  conv[volt_per_micrometer][volt_per_micrometer]         = 1.0;
+  conv[volt_per_micrometer][volt_per_nanometer]          = to_si*conv[volt_per_meter][volt_per_nanometer];
+
+  to_si = 1.0/conv[volt_per_meter][volt_per_nanometer];
+  conv[volt_per_nanometer][volt_per_meter]               = to_si*conv[volt_per_meter][volt_per_meter];
+  conv[volt_per_nanometer][volt_per_angstrom]            = to_si*conv[volt_per_meter][volt_per_angstrom];
+  conv[volt_per_nanometer][statvolt_per_centimeter]      = to_si*conv[volt_per_meter][statvolt_per_centimeter];
+  conv[volt_per_nanometer][volt_per_centimeter]          = to_si*conv[volt_per_meter][volt_per_centimeter];
+  conv[volt_per_nanometer][volt_per_micrometer]          = to_si*conv[volt_per_meter][volt_per_micrometer];
+  conv[volt_per_nanometer][volt_per_nanometer]           = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+// Demsity conversion
+double get_density_conversion_factor(units from_unit_enum, units to_unit_enum)
+{
+  map<units, map<units, double> > conv;
+  double to_si;
+
+  conv[kilogram_per_metercu][kilogram_per_metercu]           = 1.0;
+  conv[kilogram_per_metercu][gram_per_centimetercu]          = 1.0/gram_per_centimetercu_si;
+  conv[kilogram_per_metercu][amu_per_bohrcu]                 = 1.0/amu_per_bohrcu_si;
+  conv[kilogram_per_metercu][picogram_per_micrometercu]      = 1.0/picogram_per_micrometercu_si;
+  conv[kilogram_per_metercu][attogram_per_nanometercu]       = 1.0/attogram_per_nanometercu_si;
+
+  to_si = 1.0/conv[kilogram_per_metercu][gram_per_centimetercu];
+  conv[gram_per_centimetercu][kilogram_per_metercu]          = to_si*conv[kilogram_per_metercu][kilogram_per_metercu];
+  conv[gram_per_centimetercu][gram_per_centimetercu]         = 1.0;
+  conv[gram_per_centimetercu][amu_per_bohrcu]                = to_si*conv[kilogram_per_metercu][amu_per_bohrcu];
+  conv[gram_per_centimetercu][picogram_per_micrometercu]     = to_si*conv[kilogram_per_metercu][picogram_per_micrometercu];
+  conv[gram_per_centimetercu][attogram_per_nanometercu]      = to_si*conv[kilogram_per_metercu][attogram_per_nanometercu];
+
+  to_si = 1.0/conv[kilogram_per_metercu][amu_per_bohrcu];
+  conv[amu_per_bohrcu][kilogram_per_metercu]                 = to_si*conv[kilogram_per_metercu][kilogram_per_metercu];
+  conv[amu_per_bohrcu][gram_per_centimetercu]                = to_si*conv[kilogram_per_metercu][gram_per_centimetercu];
+  conv[amu_per_bohrcu][amu_per_bohrcu]                       = 1.0;
+  conv[amu_per_bohrcu][picogram_per_micrometercu]            = to_si*conv[kilogram_per_metercu][picogram_per_micrometercu];
+  conv[amu_per_bohrcu][attogram_per_nanometercu]             = to_si*conv[kilogram_per_metercu][attogram_per_nanometercu];
+
+  to_si = 1.0/conv[kilogram_per_metercu][picogram_per_micrometercu];
+  conv[picogram_per_micrometercu][kilogram_per_metercu]      = to_si*conv[kilogram_per_metercu][kilogram_per_metercu];
+  conv[picogram_per_micrometercu][gram_per_centimetercu]     = to_si*conv[kilogram_per_metercu][gram_per_centimetercu];
+  conv[picogram_per_micrometercu][amu_per_bohrcu]            = to_si*conv[kilogram_per_metercu][amu_per_bohrcu];
+  conv[picogram_per_micrometercu][picogram_per_micrometercu] = 1.0;
+  conv[picogram_per_micrometercu][attogram_per_nanometercu]  = to_si*conv[kilogram_per_metercu][attogram_per_nanometercu];
+
+  to_si = 1.0/conv[kilogram_per_metercu][attogram_per_nanometercu];
+  conv[attogram_per_nanometercu][kilogram_per_metercu]       = to_si*conv[kilogram_per_metercu][kilogram_per_metercu];
+  conv[attogram_per_nanometercu][gram_per_centimetercu]      = to_si*conv[kilogram_per_metercu][gram_per_centimetercu];
+  conv[attogram_per_nanometercu][amu_per_bohrcu]             = to_si*conv[kilogram_per_metercu][amu_per_bohrcu];
+  conv[attogram_per_nanometercu][picogram_per_micrometercu]  = to_si*conv[kilogram_per_metercu][picogram_per_micrometercu];
+  conv[attogram_per_nanometercu][attogram_per_nanometercu]   = 1.0;
+
+  return conv[from_unit_enum][to_unit_enum];
+}
+
+/* ---------------------------------------------------------------------- */
+
+//  This routine returns the unit conversion factor between the
+//  `from_system_enum` to the `to_system_enum` for the `unit_type_enum`.
+double get_unit_conversion_factor(unit_type &unit_type_enum,
+                                  sys_type from_system_enum,
+                                  sys_type to_system_enum)
+{
+  units from_unit = get_lammps_system_unit(from_system_enum, unit_type_enum);
+  units to_unit   = get_lammps_system_unit(to_system_enum, unit_type_enum);
+  switch(unit_type_enum) {
+    case mass :
+      return get_mass_conversion_factor(from_unit, to_unit);
+    case distance :
+      return get_distance_conversion_factor(from_unit, to_unit);
+    case time :
+      return get_time_conversion_factor(from_unit, to_unit);
+    case energy :
+      return get_energy_conversion_factor(from_unit, to_unit);
+    case velocity :
+      return get_velocity_conversion_factor(from_unit, to_unit);
+    case force :
+      return get_force_conversion_factor(from_unit, to_unit);
+    case torque :
+      return get_torque_conversion_factor(from_unit, to_unit);
+    case temperature :
+      return get_temperature_conversion_factor(from_unit, to_unit);
+    case pressure :
+      return get_pressure_conversion_factor(from_unit, to_unit);
+    case viscosity :
+      return get_viscosity_conversion_factor(from_unit, to_unit);
+    case charge :
+      return get_charge_conversion_factor(from_unit, to_unit);
+    case dipole :
+      return get_dipole_conversion_factor(from_unit, to_unit);
+    case efield :
+      return get_efield_conversion_factor(from_unit, to_unit);
+    case density :
+    default :    // This is here to a prevent a compiler warning
+      return get_density_conversion_factor(from_unit, to_unit);
+  }
+}
+
+} // end of anonymous name space
+
+/* ---------------------------------------------------------------------- */
+
+//  Wrapper to the routine that gets the unit conversion. Translates strings
+//  to enumerations and then call get_unit_conversion_factor()
+int lammps_unit_conversion(string const &unit_type_str,
+                           string const &from_system_str,
+                           string const &to_system_str,
+                           double &conversion_factor)
+{
+    // initialize
+    conversion_factor = 0.0;
+    initialize_dictionaries();
+
+    // convert input to enumeration
+    unit_type unit_type_enum;
+    {
+      map<string, unit_type>::const_iterator itr = unit_dic.find(unit_type_str);
+      if (itr != unit_dic.end()) unit_type_enum = itr->second;
+      else return 1;  // error
+    }
+    sys_type from_system_enum;
+    {
+      map<string, sys_type>::const_iterator
+          itr = system_dic.find(from_system_str);
+      if (itr != system_dic.end()) from_system_enum = itr->second;
+      else return 1;  // error
+    }
+    sys_type to_system_enum;
+    {
+      map<string, sys_type>::const_iterator
+          itr = system_dic.find(to_system_str);
+      if (itr != system_dic.end()) to_system_enum = itr->second;
+      else return 1;
+    }
+
+    // process unit conversions
+    conversion_factor = get_unit_conversion_factor(unit_type_enum,
+                                                   from_system_enum,
+                                                   to_system_enum);
+    return 0;
+}
+
+
diff --git a/src/KIM/kim_units.h b/src/KIM/kim_units.h
new file mode 100644
index 0000000000..97e81a6222
--- /dev/null
+++ b/src/KIM/kim_units.h
@@ -0,0 +1,59 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors: Ellad B. Tadmor (UMN)
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   This program is free software; you can redistribute it and/or modify it
+   under the terms of the GNU General Public License as published by the Free
+   Software Foundation; either version 2 of the License, or (at your option)
+   any later version.
+
+   This program is distributed in the hope that it will be useful, but WITHOUT
+   ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+   FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+   more details.
+
+   You should have received a copy of the GNU General Public License along with
+   this program; if not, see <https://www.gnu.org/licenses>.
+
+   Linking LAMMPS statically or dynamically with other modules is making a
+   combined work based on LAMMPS. Thus, the terms and conditions of the GNU
+   General Public License cover the whole combination.
+
+   In addition, as a special exception, the copyright holders of LAMMPS give
+   you permission to combine LAMMPS with free software programs or libraries
+   that are released under the GNU LGPL and with code included in the standard
+   release of the "kim-api" under the CDDL (or modified versions of such code,
+   with unchanged license). You may copy and distribute such a system following
+   the terms of the GNU GPL for LAMMPS and the licenses of the other code
+   concerned, provided that you include the source code of that other code
+   when and as the GNU GPL requires distribution of source code.
+
+   Note that people who make modified versions of LAMMPS are not obligated to
+   grant this special exception for their modified versions; it is their choice
+   whether to do so. The GNU General Public License gives permission to release
+   a modified version without this exception; this exception also makes it
+   possible to release a modified version which carries forward this exception.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Designed for use with the kim-api-2.0.2 (and newer) package
+------------------------------------------------------------------------- */
+
+int lammps_unit_conversion(std::string const &unit_type_str,
+                           std::string const &from_system_str,
+                           std::string const &to_system_str,
+                           double &conversion_factor);
diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp
index a1c13ae81f..d935d994bd 100644
--- a/src/KIM/pair_kim.cpp
+++ b/src/KIM/pair_kim.cpp
@@ -13,6 +13,7 @@
 
 /* ----------------------------------------------------------------------
    Contributing authors: Ryan S. Elliott (UMinn)
+                         Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
@@ -52,12 +53,10 @@
 /* ----------------------------------------------------------------------
    Designed for use with the kim-api-2.0.2 (and newer) package
 ------------------------------------------------------------------------- */
-
+#include "pair_kim.h"
 #include <cstring>
 #include <cstdlib>
-
-// includes from LAMMPS
-#include "pair_kim.h"
+#include <string>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -74,200 +73,184 @@ using namespace LAMMPS_NS;
 /* ---------------------------------------------------------------------- */
 
 PairKIM::PairKIM(LAMMPS *lmp) :
-   Pair(lmp),
-   settings_call_count(0),
-   init_style_call_count(0),
-   kim_modelname(NULL),
-   lmps_map_species_to_unique(NULL),
-   lmps_unique_elements(NULL),
-   lmps_num_unique_elements(0),
-   lmps_units(METAL),
-   lengthUnit(KIM_LENGTH_UNIT_unused),
-   energyUnit(KIM_ENERGY_UNIT_unused),
-   chargeUnit(KIM_CHARGE_UNIT_unused),
-   temperatureUnit(KIM_TEMPERATURE_UNIT_unused),
-   timeUnit(KIM_TIME_UNIT_unused),
-   pkim(NULL),
-   pargs(NULL),
-   kim_model_support_for_energy(KIM_SUPPORT_STATUS_notSupported),
-   kim_model_support_for_forces(KIM_SUPPORT_STATUS_notSupported),
-   kim_model_support_for_particleEnergy(KIM_SUPPORT_STATUS_notSupported),
-   kim_model_support_for_particleVirial(KIM_SUPPORT_STATUS_notSupported),
-   lmps_local_tot_num_atoms(0),
-   kim_global_influence_distance(0.0),
-   kim_number_of_neighbor_lists(0),
-   kim_cutoff_values(NULL),
-   modelWillNotRequestNeighborsOfNoncontributingParticles(NULL),
-   neighborLists(NULL),
-   kim_particle_codes(NULL),
-   lmps_maxalloc(0),
-   kim_particleSpecies(NULL),
-   kim_particleContributing(NULL),
-   lmps_stripped_neigh_list(NULL),
-   lmps_stripped_neigh_ptr(NULL)
+  Pair(lmp),
+  settings_call_count(0),
+  init_style_call_count(0),
+  kim_modelname(NULL),
+  lmps_map_species_to_unique(NULL),
+  lmps_unique_elements(NULL),
+  lmps_num_unique_elements(0),
+  lmps_units(METAL),
+  lengthUnit(KIM_LENGTH_UNIT_unused),
+  energyUnit(KIM_ENERGY_UNIT_unused),
+  chargeUnit(KIM_CHARGE_UNIT_unused),
+  temperatureUnit(KIM_TEMPERATURE_UNIT_unused),
+  timeUnit(KIM_TIME_UNIT_unused),
+  pkim(NULL),
+  pargs(NULL),
+  kim_model_support_for_energy(KIM_SUPPORT_STATUS_notSupported),
+  kim_model_support_for_forces(KIM_SUPPORT_STATUS_notSupported),
+  kim_model_support_for_particleEnergy(KIM_SUPPORT_STATUS_notSupported),
+  kim_model_support_for_particleVirial(KIM_SUPPORT_STATUS_notSupported),
+  lmps_local_tot_num_atoms(0),
+  kim_global_influence_distance(0.0),
+  kim_number_of_neighbor_lists(0),
+  kim_cutoff_values(NULL),
+  modelWillNotRequestNeighborsOfNoncontributingParticles(NULL),
+  neighborLists(NULL),
+  kim_particle_codes(NULL),
+  lmps_maxalloc(0),
+  kim_particleSpecies(NULL),
+  kim_particleContributing(NULL),
+  lmps_stripped_neigh_list(NULL),
+  lmps_stripped_neigh_ptr(NULL)
 {
-   // Initialize Pair data members to appropriate values
-   single_enable = 0;  // We do not provide the Single() function
-   restartinfo = 0;    // We do not write any restart info
-   one_coeff = 1;      // We only allow one coeff * * call
-   // set to 1, regardless use of fdotr, to avoid ev_set()'s futzing with
-   // vflag_global
-   no_virial_fdotr_compute = 1;
+  // Initialize Pair data members to appropriate values
+  single_enable = 0;  // We do not provide the Single() function
+  restartinfo = 0;    // We do not write any restart info
+  one_coeff = 1;      // We only allow one coeff * * call
+  // set to 1, regardless use of fdotr, to avoid ev_set()'s futzing with
+  // vflag_global
+  no_virial_fdotr_compute = 1;
 
-   // BEGIN: initial values that determine the KIM state
-   // (used by kim_free(), etc.)
-   kim_init_ok = false;
-   kim_particle_codes_ok = false;
-   // END
-
-   return;
+  // BEGIN: initial values that determine the KIM state
+  // (used by kim_free(), etc.)
+  kim_init_ok = false;
+  kim_particle_codes_ok = false;
+  // END
 }
 
 /* ---------------------------------------------------------------------- */
 
 PairKIM::~PairKIM()
 {
-   // clean up kim_modelname
-   if (kim_modelname != 0) delete [] kim_modelname;
+  // clean up kim_modelname
+  if (kim_modelname != 0) delete [] kim_modelname;
 
-   // clean up lammps atom species number to unique particle names mapping
-   if (lmps_unique_elements)
-      for (int i = 0; i < lmps_num_unique_elements; i++)
-        delete [] lmps_unique_elements[i];
-   delete [] lmps_unique_elements;
+  // clean up lammps atom species number to unique particle names mapping
+  if (lmps_unique_elements)
+    for (int i = 0; i < lmps_num_unique_elements; i++)
+      delete [] lmps_unique_elements[i];
+  delete [] lmps_unique_elements;
 
-   if (kim_particle_codes_ok)
-   {
-      delete [] kim_particle_codes;
-      kim_particle_codes = NULL;
-      kim_particle_codes_ok = false;
-   }
+  if (kim_particle_codes_ok) {
+    delete [] kim_particle_codes;
+    kim_particle_codes = NULL;
+    kim_particle_codes_ok = false;
+  }
 
-   // clean up local memory used to support KIM interface
-   memory->destroy(kim_particleSpecies);
-   memory->destroy(kim_particleContributing);
-   memory->destroy(lmps_stripped_neigh_list);
-   // clean up lmps_stripped_neigh_ptr
-   if (lmps_stripped_neigh_ptr)
-   {
-     delete [] lmps_stripped_neigh_ptr;
-     lmps_stripped_neigh_ptr = 0;
-   }
+  // clean up local memory used to support KIM interface
+  memory->destroy(kim_particleSpecies);
+  memory->destroy(kim_particleContributing);
+  memory->destroy(lmps_stripped_neigh_list);
+  // clean up lmps_stripped_neigh_ptr
+  if (lmps_stripped_neigh_ptr) {
+    delete [] lmps_stripped_neigh_ptr;
+    lmps_stripped_neigh_ptr = 0;
+  }
 
-   // clean up allocated memory for standard Pair class usage
-   // also, we allocate lmps_map_species_to_uniuqe in the allocate() function
-   if (allocated) {
-      memory->destroy(setflag);
-      memory->destroy(cutsq);
-      delete [] lmps_map_species_to_unique;
-   }
+  // clean up allocated memory for standard Pair class usage
+  // also, we allocate lmps_map_species_to_uniuqe in the allocate() function
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+    delete [] lmps_map_species_to_unique;
+  }
 
-   // clean up neighborlist pointers
-   if (neighborLists)
-   {
-     delete [] neighborLists;
-     neighborLists = 0;
-   }
+  // clean up neighborlist pointers
+  if (neighborLists) {
+    delete [] neighborLists;
+    neighborLists = 0;
+  }
 
-   // clean up KIM interface (if necessary)
-   kim_free();
-
-   return;
+  // clean up KIM interface (if necessary)
+  kim_free();
 }
 
 /* ---------------------------------------------------------------------- */
+
 void PairKIM::set_contributing()
 {
   int const nall = atom->nlocal + atom->nghost;
   for (int i = 0; i < nall; ++i)
-  {
     kim_particleContributing[i] = ( (i < atom->nlocal) ? 1 : 0 );
-  }
 }
 
 /* ---------------------------------------------------------------------- */
 
-void PairKIM::compute(int eflag , int vflag)
+void PairKIM::compute(int eflag, int vflag)
 {
-   ev_init(eflag,vflag);
+  ev_init(eflag,vflag);
 
-   // grow kim_particleSpecies and kim_particleContributing array if necessary
-   // needs to be atom->nmax in length
-   if (atom->nmax > lmps_maxalloc) {
-      memory->destroy(kim_particleSpecies);
-      memory->destroy(kim_particleContributing);
+  // grow kim_particleSpecies and kim_particleContributing array if necessary
+  // needs to be atom->nmax in length
+  if (atom->nmax > lmps_maxalloc) {
+    memory->destroy(kim_particleSpecies);
+    memory->destroy(kim_particleContributing);
 
-      lmps_maxalloc = atom->nmax;
-      memory->create(kim_particleSpecies,lmps_maxalloc,
-                     "pair:kim_particleSpecies");
-      int kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs,
-          KIM_COMPUTE_ARGUMENT_NAME_particleSpeciesCodes,
-          kim_particleSpecies);
-      memory->create(kim_particleContributing,lmps_maxalloc,
-                     "pair:kim_particleContributing");
-      kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerInteger(
-          pargs,
-          KIM_COMPUTE_ARGUMENT_NAME_particleContributing,
-          kim_particleContributing);
-      if (kimerror)
-        error->all(
-            FLERR,
-            "Unable to set KIM particle species codes and/or contributing");
-   }
+    lmps_maxalloc = atom->nmax;
+    memory->create(kim_particleSpecies,lmps_maxalloc,
+                   "pair:kim_particleSpecies");
+    int kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs,
+                     KIM_COMPUTE_ARGUMENT_NAME_particleSpeciesCodes,
+                     kim_particleSpecies);
+    memory->create(kim_particleContributing,lmps_maxalloc,
+                   "pair:kim_particleContributing");
+    kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerInteger(
+                             pargs,
+                             KIM_COMPUTE_ARGUMENT_NAME_particleContributing,
+                             kim_particleContributing);
+    if (kimerror)
+      error->all(FLERR,
+                 "Unable to set KIM particle species codes and/or contributing");
+  }
 
-   // kim_particleSpecies = KIM atom species for each LAMMPS atom
+  // kim_particleSpecies = KIM atom species for each LAMMPS atom
 
-   int *species = atom->type;
-   int nall = atom->nlocal + atom->nghost;
-   int ielement;
+  int *species = atom->type;
+  int nall = atom->nlocal + atom->nghost;
+  int ielement;
 
-   for (int i = 0; i < nall; i++) {
-      ielement = lmps_map_species_to_unique[species[i]];
-      kim_particleSpecies[i] = kim_particle_codes[ielement];
-   }
+  for (int i = 0; i < nall; i++) {
+    ielement = lmps_map_species_to_unique[species[i]];
+    kim_particleSpecies[i] = kim_particle_codes[ielement];
+  }
 
-   // Set kim contributing flags
-   set_contributing();
+  // Set kim contributing flags
+  set_contributing();
 
-   // pass current atom pointers to KIM
-   set_argument_pointers();
+  // pass current atom pointers to KIM
+  set_argument_pointers();
 
-   // set number of particles
-   lmps_local_tot_num_atoms = (int) nall;
+  // set number of particles
+  lmps_local_tot_num_atoms = (int) nall;
 
-   // compute via KIM model
-   int kimerror = KIM_Model_Compute(pkim, pargs);
-   if (kimerror) error->all(FLERR,"KIM Compute returned error");
+  // compute via KIM model
+  int kimerror = KIM_Model_Compute(pkim, pargs);
+  if (kimerror) error->all(FLERR,"KIM Compute returned error");
 
-   // compute virial before reverse comm!
-   if (vflag_global)
-   {
-     virial_fdotr_compute();
-   }
+  // compute virial before reverse comm!
+  if (vflag_global)
+    virial_fdotr_compute();
 
-   // if newton is off, perform reverse comm
-   if (!lmps_using_newton)
-   {
-     comm->reverse_comm_pair(this);
-   }
+  // if newton is off, perform reverse comm
+  if (!lmps_using_newton) {
+    comm->reverse_comm_pair(this);
+  }
 
-   if ((vflag_atom) &&
-       KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial,
-                                  KIM_SUPPORT_STATUS_notSupported)
-      )
-   {  // flip sign and order of virial if KIM is computing it
-      double tmp;
-      for (int i = 0; i < nall; ++i)
-      {
-         for (int j = 0; j < 3; ++j) vatom[i][j] = -1.0*vatom[i][j];
-         tmp = vatom[i][3];
-         vatom[i][3] = -vatom[i][5];
-         vatom[i][4] = -vatom[i][4];
-         vatom[i][5] = -tmp;
-      }
-   }
-
-   return;
+  if ((vflag_atom) &&
+      KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial,
+                                 KIM_SUPPORT_STATUS_notSupported)) {
+    // flip sign and order of virial if KIM is computing it
+    double tmp;
+    for (int i = 0; i < nall; ++i) {
+      for (int j = 0; j < 3; ++j) vatom[i][j] = -1.0*vatom[i][j];
+      tmp = vatom[i][3];
+      vatom[i][3] = -vatom[i][5];
+      vatom[i][4] = -vatom[i][4];
+      vatom[i][5] = -tmp;
+    }
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -276,22 +259,20 @@ void PairKIM::compute(int eflag , int vflag)
 
 void PairKIM::allocate()
 {
-   int n = atom->ntypes;
+  int n = atom->ntypes;
 
-   // allocate standard Pair class arrays
-   memory->create(setflag,n+1,n+1,"pair:setflag");
-   for (int i = 1; i <= n; i++)
-     for (int j = i; j <= n; j++)
-       setflag[i][j] = 0;
+  // allocate standard Pair class arrays
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
 
-   memory->create(cutsq,n+1,n+1,"pair:cutsq");
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
 
-   // allocate mapping array
-   lmps_map_species_to_unique = new int[n+1];
+  // allocate mapping array
+  lmps_map_species_to_unique = new int[n+1];
 
-   allocated = 1;
-
-   return;
+  allocated = 1;
 }
 
 /* ----------------------------------------------------------------------
@@ -300,56 +281,49 @@ void PairKIM::allocate()
 
 void PairKIM::settings(int narg, char **arg)
 {
-   // This is called when "pair_style kim ..." is read from input
-   // may be called multiple times
-   ++settings_call_count;
-   init_style_call_count = 0;
+  // This is called when "pair_style kim ..." is read from input
+  // may be called multiple times
+  ++settings_call_count;
+  init_style_call_count = 0;
 
-   if (narg != 1)
-   {
-     if ((narg > 0) && ((0 == strcmp("KIMvirial", arg[0])) ||
-                        (0 == strcmp("LAMMPSvirial", arg[0]))))
-     {
-       error->all(FLERR,"'KIMvirial' or 'LAMMPSvirial' not supported with "
-                  "kim-api.");
-     }
-     else
-       error->all(FLERR,"Illegal pair_style command");
-   }
-   // arg[0] is the KIM Model name
+  if (narg != 1) {
+    if ((narg > 0) && ((0 == strcmp("KIMvirial", arg[0])) ||
+                       (0 == strcmp("LAMMPSvirial", arg[0])))) {
+      error->all(FLERR,"'KIMvirial' or 'LAMMPSvirial' not supported with "
+                 "kim-api.");
+    } else error->all(FLERR,"Illegal pair_style command");
+  }
+  // arg[0] is the KIM Model name
 
-   lmps_using_molecular = (atom->molecular > 0);
+  lmps_using_molecular = (atom->molecular > 0);
 
-   // ensure we are in a clean state for KIM (needed on repeated call)
-   // first time called will do nothing...
-   kim_free();
+  // ensure we are in a clean state for KIM (needed on repeated call)
+  // first time called will do nothing...
+  kim_free();
 
-   // make sure things are allocated
-   if (allocated != 1) allocate();
+  // make sure things are allocated
+  if (allocated != 1) allocate();
 
-   // clear setflag to ensure coeff() is called after settings()
-   int n = atom->ntypes;
-   for (int i = 1; i <= n; i++)
-      for (int j = i; j <= n; j++)
-         setflag[i][j] = 0;
+  // clear setflag to ensure coeff() is called after settings()
+  int n = atom->ntypes;
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
 
-    // set lmps_* bool flags
-   set_lmps_flags();
+  // set lmps_* bool flags
+  set_lmps_flags();
 
-   // set KIM Model name
-   int nmlen = strlen(arg[0]);
-   if (kim_modelname != 0)
-   {
-      delete [] kim_modelname;
-      kim_modelname = 0;
-   }
-   kim_modelname = new char[nmlen+1];
-   strcpy(kim_modelname, arg[0]);
+  // set KIM Model name
+  int nmlen = strlen(arg[0]);
+  if (kim_modelname != 0) {
+    delete [] kim_modelname;
+    kim_modelname = 0;
+  }
+  kim_modelname = new char[nmlen+1];
+  strcpy(kim_modelname, arg[0]);
 
-   // initialize KIM Model
-   kim_init();
-
-   return;
+  // initialize KIM Model
+  kim_init();
 }
 
 /* ----------------------------------------------------------------------
@@ -358,99 +332,95 @@ void PairKIM::settings(int narg, char **arg)
 
 void PairKIM::coeff(int narg, char **arg)
 {
-   // This is called when "pair_coeff ..." is read from input
-   // may be called multiple times
+  // This is called when "pair_coeff ..." is read from input
+  // may be called multiple times
 
-   int i,j,n;
+  int i,j,n;
 
-   if (!allocated) allocate();
+  if (!allocated) allocate();
 
-   if (narg != 2 + atom->ntypes)
-      error->all(FLERR,"Incorrect args for pair coefficients");
+  if (narg != 2 + atom->ntypes)
+    error->all(FLERR,"Incorrect args for pair coefficients");
 
-   // insure I,J args are * *
+  // insure I,J args are * *
 
-   if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
-     error->all(FLERR,"Incorrect args for pair coefficients");
+  if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
+    error->all(FLERR,"Incorrect args for pair coefficients");
 
+  int ilo,ihi,jlo,jhi;
+  force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+  force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
 
-   int ilo,ihi,jlo,jhi;
-   force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
-   force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+  // read args that map atom species to KIM elements
+  // lmps_map_species_to_unique[i] =
+  // which element the Ith atom type is
+  // lmps_num_unique_elements = # of unique elements
+  // lmps_unique_elements = list of element names
 
-   // read args that map atom species to KIM elements
-   // lmps_map_species_to_unique[i] =
-   // which element the Ith atom type is
-   // lmps_num_unique_elements = # of unique elements
-   // lmps_unique_elements = list of element names
+  // if called multiple times: update lmps_unique_elements
+  if (lmps_unique_elements) {
+    for (i = 0; i < lmps_num_unique_elements; i++)
+      delete [] lmps_unique_elements[i];
+    delete [] lmps_unique_elements;
+  }
+  lmps_unique_elements = new char*[atom->ntypes];
+  for (i = 0; i < atom->ntypes; i++) lmps_unique_elements[i] = 0;
 
-   // if called multiple times: update lmps_unique_elements
-   if (lmps_unique_elements) {
-      for (i = 0; i < lmps_num_unique_elements; i++)
-        delete [] lmps_unique_elements[i];
-      delete [] lmps_unique_elements;
-   }
-   lmps_unique_elements = new char*[atom->ntypes];
-   for (i = 0; i < atom->ntypes; i++) lmps_unique_elements[i] = 0;
+  // Assume all species arguments are valid
+  // errors will be detected by below
+  std::string atom_type_sym_list;
+  lmps_num_unique_elements = 0;
+  for (i = 2; i < narg; i++) {
+    atom_type_sym_list += std::string(" ") + arg[i];
+    for (j = 0; j < lmps_num_unique_elements; j++)
+      if (strcmp(arg[i],lmps_unique_elements[j]) == 0) break;
+    lmps_map_species_to_unique[i-1] = j;
+    if (j == lmps_num_unique_elements) {
+      n = strlen(arg[i]) + 1;
+      lmps_unique_elements[j] = new char[n];
+      strcpy(lmps_unique_elements[j],arg[i]);
+      lmps_num_unique_elements++;
+    }
+  }
 
-
-   // Assume all species arguments are valid
-   // errors will be detected by below
-   lmps_num_unique_elements = 0;
-   for (i = 2; i < narg; i++) {
-     for (j = 0; j < lmps_num_unique_elements; j++)
-       if (strcmp(arg[i],lmps_unique_elements[j]) == 0) break;
-     lmps_map_species_to_unique[i-1] = j;
-     if (j == lmps_num_unique_elements) {
-       n = strlen(arg[i]) + 1;
-       lmps_unique_elements[j] = new char[n];
-       strcpy(lmps_unique_elements[j],arg[i]);
-       lmps_num_unique_elements++;
-     }
-   }
-
-   int count = 0;
-   for (int i = ilo; i <= ihi; i++) {
-     for (int j = MAX(jlo,i); j <= jhi; j++) {
-       if (lmps_map_species_to_unique[i] >= 0 &&
-           lmps_map_species_to_unique[j] >= 0) {
-         setflag[i][j] = 1;
-         count++;
-       }
-     }
-   }
-
-   if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
-
-   // setup mapping between LAMMPS unique elements and KIM species codes
-   if (kim_particle_codes_ok)
-   {
-     delete [] kim_particle_codes;
-     kim_particle_codes = NULL;
-     kim_particle_codes_ok = false;
-   }
-   kim_particle_codes = new int[lmps_num_unique_elements];
-   kim_particle_codes_ok = true;
-   for(int i = 0; i < lmps_num_unique_elements; i++){
-      int supported;
-      int code;
-      KIM_Model_GetSpeciesSupportAndCode(
-          pkim,
-          KIM_SpeciesName_FromString(lmps_unique_elements[i]),
-          &supported,
-          &code);
-      if (supported)
-        kim_particle_codes[i] = code;
-      else
-      {
-        std::stringstream msg;
-        msg << "create_kim_particle_codes: symbol not found: "
-            << lmps_unique_elements[i];
-        error->all(FLERR, msg.str().c_str());
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo,i); j <= jhi; j++) {
+      if (lmps_map_species_to_unique[i] >= 0 &&
+          lmps_map_species_to_unique[j] >= 0) {
+        setflag[i][j] = 1;
+        count++;
       }
-   }
+    }
+  }
 
-   return;
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+
+  // setup mapping between LAMMPS unique elements and KIM species codes
+  if (kim_particle_codes_ok) {
+    delete [] kim_particle_codes;
+    kim_particle_codes = NULL;
+    kim_particle_codes_ok = false;
+  }
+  kim_particle_codes = new int[lmps_num_unique_elements];
+  kim_particle_codes_ok = true;
+
+  for(int i = 0; i < lmps_num_unique_elements; i++) {
+    int supported;
+    int code;
+    KIM_Model_GetSpeciesSupportAndCode(
+      pkim,
+      KIM_SpeciesName_FromString(lmps_unique_elements[i]),
+      &supported,
+      &code);
+    if (supported) {
+      kim_particle_codes[i] = code;
+    } else {
+      std::string msg("create_kim_particle_codes: symbol not found: ");
+      msg += lmps_unique_elements[i];
+      error->all(FLERR, msg.c_str());
+    }
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -459,57 +429,48 @@ void PairKIM::coeff(int narg, char **arg)
 
 void PairKIM::init_style()
 {
-   // This is called for each "run ...", "minimize ...", etc. read from input
-   ++init_style_call_count;
+  // This is called for each "run ...", "minimize ...", etc. read from input
+  ++init_style_call_count;
 
-   if (domain->dimension != 3)
-      error->all(FLERR,"PairKIM only works with 3D problems");
+  if (domain->dimension != 3)
+    error->all(FLERR,"PairKIM only works with 3D problems");
 
-   // setup lmps_stripped_neigh_list for neighbors of one atom, if needed
-   if (lmps_using_molecular) {
-      memory->destroy(lmps_stripped_neigh_list);
-      memory->create(lmps_stripped_neigh_list,
-                     kim_number_of_neighbor_lists*neighbor->oneatom,
-                     "pair:lmps_stripped_neigh_list");
-      delete [] lmps_stripped_neigh_ptr;
-      lmps_stripped_neigh_ptr = new int*[kim_number_of_neighbor_lists];
-      for (int i = 0; i < kim_number_of_neighbor_lists; ++i)
-      {
-        lmps_stripped_neigh_ptr[i]
-            = &(lmps_stripped_neigh_list[i*(neighbor->oneatom)]);
-      }
+  // setup lmps_stripped_neigh_list for neighbors of one atom, if needed
+  if (lmps_using_molecular) {
+    memory->destroy(lmps_stripped_neigh_list);
+    memory->create(lmps_stripped_neigh_list,
+                   kim_number_of_neighbor_lists*neighbor->oneatom,
+                   "pair:lmps_stripped_neigh_list");
+    delete [] lmps_stripped_neigh_ptr;
+    lmps_stripped_neigh_ptr = new int*[kim_number_of_neighbor_lists];
+    for (int i = 0; i < kim_number_of_neighbor_lists; ++i)
+      lmps_stripped_neigh_ptr[i]
+        = &(lmps_stripped_neigh_list[i*(neighbor->oneatom)]);
+  }
 
-   }
+  // make sure comm_reverse expects (at most) 9 values when newton is off
+  if (!lmps_using_newton) comm_reverse_off = 9;
 
-   // make sure comm_reverse expects (at most) 9 values when newton is off
-   if (!lmps_using_newton) comm_reverse_off = 9;
+  // request full neighbor
+  for (int i = 0; i < kim_number_of_neighbor_lists; ++i) {
+    int irequest = neighbor->request(this,instance_me);
+    neighbor->requests[irequest]->id = i;
+    neighbor->requests[irequest]->half = 0;
+    neighbor->requests[irequest]->full = 1;
 
-   // request full neighbor
-   for (int i = 0; i < kim_number_of_neighbor_lists; ++i)
-   {
-     int irequest = neighbor->request(this,instance_me);
-     neighbor->requests[irequest]->id = i;
-     neighbor->requests[irequest]->half = 0;
-     neighbor->requests[irequest]->full = 1;
+    if (modelWillNotRequestNeighborsOfNoncontributingParticles[i])
+      neighbor->requests[irequest]->ghost = 0;
+    else
+      neighbor->requests[irequest]->ghost = 1;
 
-     if (modelWillNotRequestNeighborsOfNoncontributingParticles[i])
-     {
-       neighbor->requests[irequest]->ghost = 0;
-     }
-     else
-     {
-       neighbor->requests[irequest]->ghost = 1;
+    // always want all owned/ghost pairs
+    neighbor->requests[irequest]->newton = 2;
 
-     }
-     // always want all owned/ghost pairs
-     neighbor->requests[irequest]->newton = 2;
-     // set cutoff
-     neighbor->requests[irequest]->cut = 1;
-     neighbor->requests[irequest]->cutoff
-         = kim_cutoff_values[i] + neighbor->skin;
-   }
-
-   return;
+    // set cutoff
+    neighbor->requests[irequest]->cut = 1;
+    neighbor->requests[irequest]->cutoff
+      = kim_cutoff_values[i] + neighbor->skin;
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -528,154 +489,134 @@ void PairKIM::init_list(int id, NeighList *ptr)
 
 double PairKIM::init_one(int i, int j)
 {
-   // This is called once of each (unordered) i,j pair for each
-   // "run ...", "minimize ...", etc. read from input
+  // This is called once of each (unordered) i,j pair for each
+  // "run ...", "minimize ...", etc. read from input
 
-   if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
 
-   return kim_global_influence_distance;
+  return kim_global_influence_distance;
 }
 
 /* ---------------------------------------------------------------------- */
 
 int PairKIM::pack_reverse_comm(int n, int first, double *buf)
 {
-   int i,m,last;
-   double *fp;
-   fp = &(atom->f[0][0]);
+  int i,m,last;
+  double *fp;
+  fp = &(atom->f[0][0]);
 
-   m = 0;
-   last = first + n;
-   if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces,
-                                  KIM_SUPPORT_STATUS_notSupported)
-       &&
-       ((vflag_atom == 0) ||
-        KIM_SupportStatus_Equal(kim_model_support_for_particleVirial,
-                                KIM_SUPPORT_STATUS_notSupported)))
-   {
-      for (i = first; i < last; i++)
-      {
-         buf[m++] = fp[3*i+0];
-         buf[m++] = fp[3*i+1];
-         buf[m++] = fp[3*i+2];
-      }
-      return m;
-   }
-   else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces,
-                                       KIM_SUPPORT_STATUS_notSupported) &&
-            (vflag_atom == 1) &&
-            KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial,
-                                       KIM_SUPPORT_STATUS_notSupported))
-   {
-      double *va=&(vatom[0][0]);
-      for (i = first; i < last; i++)
-      {
-         buf[m++] = fp[3*i+0];
-         buf[m++] = fp[3*i+1];
-         buf[m++] = fp[3*i+2];
+  m = 0;
+  last = first + n;
+  if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces,
+                                 KIM_SUPPORT_STATUS_notSupported)
+      &&
+      ((vflag_atom == 0) ||
+       KIM_SupportStatus_Equal(kim_model_support_for_particleVirial,
+                               KIM_SUPPORT_STATUS_notSupported))) {
+    for (i = first; i < last; i++) {
+      buf[m++] = fp[3*i+0];
+      buf[m++] = fp[3*i+1];
+      buf[m++] = fp[3*i+2];
+    }
+    return m;
+  } else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces,
+                                        KIM_SUPPORT_STATUS_notSupported) &&
+             (vflag_atom == 1) &&
+             KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial,
+                                        KIM_SUPPORT_STATUS_notSupported)) {
+    double *va=&(vatom[0][0]);
+    for (i = first; i < last; i++) {
+      buf[m++] = fp[3*i+0];
+      buf[m++] = fp[3*i+1];
+      buf[m++] = fp[3*i+2];
 
-         buf[m++] = va[6*i+0];
-         buf[m++] = va[6*i+1];
-         buf[m++] = va[6*i+2];
-         buf[m++] = va[6*i+3];
-         buf[m++] = va[6*i+4];
-         buf[m++] = va[6*i+5];
-      }
-      return m;
-   }
-   else if (KIM_SupportStatus_Equal(kim_model_support_for_forces,
-                                    KIM_SUPPORT_STATUS_notSupported)
-            &&
-            (vflag_atom == 1) &&
-            KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial,
-                                       KIM_SUPPORT_STATUS_notSupported))
-   {
-      double *va=&(vatom[0][0]);
-      for (i = first; i < last; i++)
-      {
-         buf[m++] = va[6*i+0];
-         buf[m++] = va[6*i+1];
-         buf[m++] = va[6*i+2];
-         buf[m++] = va[6*i+3];
-         buf[m++] = va[6*i+4];
-         buf[m++] = va[6*i+5];
-      }
-      return m;
-   }
-   else
-      return 0;
+      buf[m++] = va[6*i+0];
+      buf[m++] = va[6*i+1];
+      buf[m++] = va[6*i+2];
+      buf[m++] = va[6*i+3];
+      buf[m++] = va[6*i+4];
+      buf[m++] = va[6*i+5];
+    }
+    return m;
+  } else if (KIM_SupportStatus_Equal(kim_model_support_for_forces,
+                                     KIM_SUPPORT_STATUS_notSupported)
+             &&
+             (vflag_atom == 1) &&
+             KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial,
+                                        KIM_SUPPORT_STATUS_notSupported)) {
+    double *va=&(vatom[0][0]);
+    for (i = first; i < last; i++) {
+      buf[m++] = va[6*i+0];
+      buf[m++] = va[6*i+1];
+      buf[m++] = va[6*i+2];
+      buf[m++] = va[6*i+3];
+      buf[m++] = va[6*i+4];
+      buf[m++] = va[6*i+5];
+    }
+    return m;
+  } else return 0;
 }
 
 /* ---------------------------------------------------------------------- */
 
 void PairKIM::unpack_reverse_comm(int n, int *list, double *buf)
 {
-   int i,j,m;
-   double *fp;
-   fp = &(atom->f[0][0]);
+  int i,j,m;
+  double *fp;
+  fp = &(atom->f[0][0]);
 
-   m = 0;
-   if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces,
-                                  KIM_SUPPORT_STATUS_notSupported)
-       &&
-       ((vflag_atom == 0) ||
-        KIM_SupportStatus_Equal(kim_model_support_for_particleVirial,
-                                KIM_SUPPORT_STATUS_notSupported)))
-   {
-      for (i = 0; i < n; i++)
-      {
-         j = list[i];
-         fp[3*j+0]+= buf[m++];
-         fp[3*j+1]+= buf[m++];
-         fp[3*j+2]+= buf[m++];
-      }
-   }
-   else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces,
-                                       KIM_SUPPORT_STATUS_notSupported)
-            &&
-            (vflag_atom == 1) &&
-            KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial,
-                                       KIM_SUPPORT_STATUS_notSupported))
-   {
-      double *va=&(vatom[0][0]);
-      for (i = 0; i < n; i++)
-      {
-         j = list[i];
-         fp[3*j+0]+= buf[m++];
-         fp[3*j+1]+= buf[m++];
-         fp[3*j+2]+= buf[m++];
+  m = 0;
+  if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces,
+                                 KIM_SUPPORT_STATUS_notSupported)
+      &&
+      ((vflag_atom == 0) ||
+       KIM_SupportStatus_Equal(kim_model_support_for_particleVirial,
+                               KIM_SUPPORT_STATUS_notSupported))) {
+    for (i = 0; i < n; i++) {
+      j = list[i];
+      fp[3*j+0]+= buf[m++];
+      fp[3*j+1]+= buf[m++];
+      fp[3*j+2]+= buf[m++];
+    }
+  } else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces,
+                                        KIM_SUPPORT_STATUS_notSupported)
+             &&
+             (vflag_atom == 1) &&
+             KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial,
+                                        KIM_SUPPORT_STATUS_notSupported)) {
+    double *va=&(vatom[0][0]);
+    for (i = 0; i < n; i++) {
+      j = list[i];
+      fp[3*j+0]+= buf[m++];
+      fp[3*j+1]+= buf[m++];
+      fp[3*j+2]+= buf[m++];
 
-         va[j*6+0]+=buf[m++];
-         va[j*6+1]+=buf[m++];
-         va[j*6+2]+=buf[m++];
-         va[j*6+3]+=buf[m++];
-         va[j*6+4]+=buf[m++];
-         va[j*6+5]+=buf[m++];
-      }
-   }
-   else if (KIM_SupportStatus_Equal(kim_model_support_for_forces,
-                                    KIM_SUPPORT_STATUS_notSupported)
-            &&
-            (vflag_atom == 1) &&
-            KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial,
-                                       KIM_SUPPORT_STATUS_notSupported))
-   {
-      double *va=&(vatom[0][0]);
-      for (i = 0; i < n; i++)
-      {
-         j = list[i];
-         va[j*6+0]+=buf[m++];
-         va[j*6+1]+=buf[m++];
-         va[j*6+2]+=buf[m++];
-         va[j*6+3]+=buf[m++];
-         va[j*6+4]+=buf[m++];
-         va[j*6+5]+=buf[m++];
-      }
-   } else {
-     ; // do nothing
-   }
-
-   return;
+      va[j*6+0]+=buf[m++];
+      va[j*6+1]+=buf[m++];
+      va[j*6+2]+=buf[m++];
+      va[j*6+3]+=buf[m++];
+      va[j*6+4]+=buf[m++];
+      va[j*6+5]+=buf[m++];
+    }
+  } else if (KIM_SupportStatus_Equal(kim_model_support_for_forces,
+                                     KIM_SUPPORT_STATUS_notSupported)
+             &&
+             (vflag_atom == 1) &&
+             KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial,
+                                        KIM_SUPPORT_STATUS_notSupported)) {
+    double *va=&(vatom[0][0]);
+    for (i = 0; i < n; i++) {
+      j = list[i];
+      va[j*6+0]+=buf[m++];
+      va[j*6+1]+=buf[m++];
+      va[j*6+2]+=buf[m++];
+      va[j*6+3]+=buf[m++];
+      va[j*6+4]+=buf[m++];
+      va[j*6+5]+=buf[m++];
+    }
+  } else {
+    ; // do nothing
+  }
 }
 
 /* ----------------------------------------------------------------------
@@ -684,8 +625,8 @@ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf)
 
 double PairKIM::memory_usage()
 {
-   double bytes = 2 * lmps_maxalloc * sizeof(int);
-   return bytes;
+  double bytes = 2 * lmps_maxalloc * sizeof(int);
+  return bytes;
 }
 
 /* ----------------------------------------------------------------------
@@ -695,142 +636,123 @@ double PairKIM::memory_usage()
 int PairKIM::get_neigh(void const * const dataObject,
                        int const numberOfNeighborLists,
                        double const * const cutoffs,
-                       int const neighborListIndex, int const particleNumber,
+                       int const neighborListIndex,
+                       int const particleNumber,
                        int * const numberOfNeighbors,
                        int const ** const neighborsOfParticle)
 {
-   PairKIM const * const Model
-       = reinterpret_cast<PairKIM const * const>(dataObject);
+  PairKIM const * const Model
+    = reinterpret_cast<PairKIM const * const>(dataObject);
 
-   if (numberOfNeighborLists != Model->kim_number_of_neighbor_lists)
-     return true;
-   for (int i = 0; i < numberOfNeighborLists; ++i)
-   {
-     if (Model->kim_cutoff_values[i] < cutoffs[i]) return true;
-   }
+  if (numberOfNeighborLists != Model->kim_number_of_neighbor_lists)
+    return true;
+  for (int i = 0; i < numberOfNeighborLists; ++i) {
+    if (Model->kim_cutoff_values[i] < cutoffs[i]) return true;
+  }
 
-   // neighborListIndex and particleNumber are validated by KIM API
+  // neighborListIndex and particleNumber are validated by KIM API
 
-   // initialize numNeigh
-   *numberOfNeighbors = 0;
+  // initialize numNeigh
+  *numberOfNeighbors = 0;
 
-   NeighList * neiobj = Model->neighborLists[neighborListIndex];
+  NeighList * neiobj = Model->neighborLists[neighborListIndex];
 
-   int *numneigh, **firstneigh;
-   numneigh = neiobj->numneigh;     // # of J neighbors for each I atom
-   firstneigh = neiobj->firstneigh; // ptr to 1st J int value of each I atom
+  int *numneigh, **firstneigh;
+  numneigh = neiobj->numneigh;     // # of J neighbors for each I atom
+  firstneigh = neiobj->firstneigh; // ptr to 1st J int value of each I atom
 
-   *numberOfNeighbors = numneigh[particleNumber];
+  *numberOfNeighbors = numneigh[particleNumber];
 
-   // strip off neighbor mask for molecular systems
-   if (!Model->lmps_using_molecular)
-     *neighborsOfParticle = firstneigh[particleNumber];
-   else
-   {
-     int n = *numberOfNeighbors;
-     int *ptr = firstneigh[particleNumber];
-     int *lmps_stripped_neigh_list
-         = Model->lmps_stripped_neigh_ptr[neighborListIndex];
-     for (int i = 0; i < n; i++)
-       lmps_stripped_neigh_list[i] = *(ptr++) & NEIGHMASK;
-     *neighborsOfParticle = lmps_stripped_neigh_list;
-   }
-   return false;
+  // strip off neighbor mask for molecular systems
+  if (!Model->lmps_using_molecular)
+    *neighborsOfParticle = firstneigh[particleNumber];
+  else {
+    int n = *numberOfNeighbors;
+    int *ptr = firstneigh[particleNumber];
+    int *lmps_stripped_neigh_list
+      = Model->lmps_stripped_neigh_ptr[neighborListIndex];
+    for (int i = 0; i < n; i++)
+      lmps_stripped_neigh_list[i] = *(ptr++) & NEIGHMASK;
+    *neighborsOfParticle = lmps_stripped_neigh_list;
+  }
+  return false;
 }
 
 /* ---------------------------------------------------------------------- */
 
 void PairKIM::kim_free()
 {
-   if (kim_init_ok)
-   {
-     int kimerror = KIM_Model_ComputeArgumentsDestroy(pkim, &pargs);
-     if (kimerror)
-       error->all(FLERR,"Unable to destroy Compute Arguments Object");
+  if (kim_init_ok) {
+    int kimerror = KIM_Model_ComputeArgumentsDestroy(pkim, &pargs);
+    if (kimerror)
+      error->all(FLERR,"Unable to destroy Compute Arguments Object");
 
-     KIM_Model_Destroy(&pkim);
-   }
-   kim_init_ok = false;
-
-   return;
+    KIM_Model_Destroy(&pkim);
+  }
+  kim_init_ok = false;
 }
 
 /* ---------------------------------------------------------------------- */
 
 void PairKIM::kim_init()
 {
-   int kimerror;
+  int kimerror;
 
-   // initialize KIM model
-   int requestedUnitsAccepted;
-   kimerror = KIM_Model_Create(
-       KIM_NUMBERING_zeroBased,
-       lengthUnit, energyUnit, chargeUnit, temperatureUnit, timeUnit,
-       kim_modelname,
-       &requestedUnitsAccepted,
-       &pkim);
-   if (kimerror)
-     error->all(FLERR,"KIM ModelCreate failed");
-   else {
-     if (!requestedUnitsAccepted) {
-       error->all(FLERR,"KIM Model did not accept the requested unit system");
-     }
+  // initialize KIM model
+  int requestedUnitsAccepted;
+  kimerror = KIM_Model_Create(
+    KIM_NUMBERING_zeroBased,
+    lengthUnit, energyUnit, chargeUnit, temperatureUnit, timeUnit,
+    kim_modelname,
+    &requestedUnitsAccepted,
+    &pkim);
+  if (kimerror) error->all(FLERR,"KIM ModelCreate failed");
+  else if (!requestedUnitsAccepted)
+    error->all(FLERR,"KIM Model did not accept the requested unit system");
 
-     // check that the model does not require unknown capabilities
-     kimerror = check_for_routine_compatibility();
-     if (kimerror)
-     {
-       error->all(FLERR,
-                  "KIM Model requires unknown Routines.  Unable to proceed.");
-     }
+  // check that the model does not require unknown capabilities
+  kimerror = check_for_routine_compatibility();
+  if (kimerror)
+    error->all(FLERR,
+               "KIM Model requires unknown Routines.  Unable to proceed.");
 
-     kimerror = KIM_Model_ComputeArgumentsCreate(pkim, &pargs);
-     if (kimerror)
-     {
-       KIM_Model_Destroy(&pkim);
-       error->all(FLERR,"KIM ComputeArgumentsCreate failed");
-     }
-     else
-     {
-       kim_init_ok = true;
-     }
-   }
+  kimerror = KIM_Model_ComputeArgumentsCreate(pkim, &pargs);
+  if (kimerror) {
+    KIM_Model_Destroy(&pkim);
+    error->all(FLERR,"KIM ComputeArgumentsCreate failed");
+  } else kim_init_ok = true;
 
-   // determine KIM Model capabilities (used in this function below)
-   set_kim_model_has_flags();
+  // determine KIM Model capabilities (used in this function below)
+  set_kim_model_has_flags();
 
-   KIM_Model_GetInfluenceDistance(pkim, &kim_global_influence_distance);
-   KIM_Model_GetNeighborListPointers(
-       pkim,
-       &kim_number_of_neighbor_lists,
-       &kim_cutoff_values,
-       &modelWillNotRequestNeighborsOfNoncontributingParticles);
-   if (neighborLists)
-   {
-     delete [] neighborLists;
-     neighborLists = 0;
-   }
-   neighborLists = new NeighList*[kim_number_of_neighbor_lists];
+  KIM_Model_GetInfluenceDistance(pkim, &kim_global_influence_distance);
+  KIM_Model_GetNeighborListPointers(
+    pkim,
+    &kim_number_of_neighbor_lists,
+    &kim_cutoff_values,
+    &modelWillNotRequestNeighborsOfNoncontributingParticles);
+  if (neighborLists) {
+    delete [] neighborLists;
+    neighborLists = 0;
+  }
+  neighborLists = new NeighList*[kim_number_of_neighbor_lists];
 
-   kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs,
-       KIM_COMPUTE_ARGUMENT_NAME_numberOfParticles,
-       &lmps_local_tot_num_atoms);
-   if (KIM_SupportStatus_NotEqual(kim_model_support_for_energy,
-                                  KIM_SUPPORT_STATUS_notSupported))
-     kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(pargs,
-         KIM_COMPUTE_ARGUMENT_NAME_partialEnergy,
-         &(eng_vdwl));
+  kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs,
+    KIM_COMPUTE_ARGUMENT_NAME_numberOfParticles,
+    &lmps_local_tot_num_atoms);
+  if (KIM_SupportStatus_NotEqual(kim_model_support_for_energy,
+                                 KIM_SUPPORT_STATUS_notSupported))
+    kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(pargs,
+      KIM_COMPUTE_ARGUMENT_NAME_partialEnergy,
+      &(eng_vdwl));
 
-   kimerror = KIM_ComputeArguments_SetCallbackPointer(pargs,
-       KIM_COMPUTE_CALLBACK_NAME_GetNeighborList,
-       KIM_LANGUAGE_NAME_cpp,
-       reinterpret_cast<KIM_Function *>(get_neigh),
-       reinterpret_cast<void *>(this));
+  kimerror = KIM_ComputeArguments_SetCallbackPointer(pargs,
+    KIM_COMPUTE_CALLBACK_NAME_GetNeighborList,
+    KIM_LANGUAGE_NAME_cpp,
+    reinterpret_cast<KIM_Function *>(get_neigh),
+    reinterpret_cast<void *>(this));
 
-   if (kimerror)
-     error->all(FLERR,"Unable to register KIM pointers");
-
-   return;
+  if (kimerror) error->all(FLERR,"Unable to register KIM pointers");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -839,16 +761,14 @@ void PairKIM::set_argument_pointers()
 {
   int kimerror;
   kimerror = KIM_ComputeArguments_SetArgumentPointerDouble(
-      pargs, KIM_COMPUTE_ARGUMENT_NAME_coordinates, &(atom->x[0][0]));
+    pargs, KIM_COMPUTE_ARGUMENT_NAME_coordinates, &(atom->x[0][0]));
 
   // Set KIM pointer appropriately for particalEnergy
   if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy,
                               KIM_SUPPORT_STATUS_required)
-      && (eflag_atom != 1))
-  {
+      && (eflag_atom != 1)) {
     // reallocate per-atom energy array if necessary
-    if (atom->nmax > maxeatom)
-    {
+    if (atom->nmax > maxeatom) {
       maxeatom = atom->nmax;
       memory->destroy(eatom);
       memory->create(eatom,comm->nthreads*maxeatom,"pair:eatom");
@@ -856,31 +776,25 @@ void PairKIM::set_argument_pointers()
   }
   if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy,
                               KIM_SUPPORT_STATUS_optional)
-      && (eflag_atom != 1))
-  {
+      && (eflag_atom != 1)) {
     kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(
-        pargs,
-        KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy,
-        reinterpret_cast<double * const>(NULL));
-  }
-  else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleEnergy,
-                                      KIM_SUPPORT_STATUS_notSupported))
-  {
+      pargs,
+      KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy,
+      reinterpret_cast<double * const>(NULL));
+  } else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleEnergy,
+                                      KIM_SUPPORT_STATUS_notSupported)) {
     kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(
         pargs, KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, eatom);
   }
 
   // Set KIM pointer appropriately for forces
   if (KIM_SupportStatus_Equal(kim_model_support_for_forces,
-                              KIM_SUPPORT_STATUS_notSupported))
-  {
+                              KIM_SUPPORT_STATUS_notSupported)) {
     kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(
-        pargs,
-        KIM_COMPUTE_ARGUMENT_NAME_partialForces,
-        reinterpret_cast<double * const>(NULL));
-  }
-  else
-  {
+      pargs,
+      KIM_COMPUTE_ARGUMENT_NAME_partialForces,
+      reinterpret_cast<double * const>(NULL));
+  } else {
     kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(
         pargs, KIM_COMPUTE_ARGUMENT_NAME_partialForces, &(atom->f[0][0]));
   }
@@ -888,11 +802,9 @@ void PairKIM::set_argument_pointers()
   // Set KIM pointer appropriately for particleVirial
   if (KIM_SupportStatus_Equal(kim_model_support_for_particleVirial,
                               KIM_SUPPORT_STATUS_required)
-      && (vflag_atom != 1))
-  {
+      && (vflag_atom != 1)) {
     // reallocate per-atom virial array if necessary
-    if (atom->nmax > maxeatom)
-    {
+    if (atom->nmax > maxeatom) {
       maxvatom = atom->nmax;
       memory->destroy(vatom);
       memory->create(vatom,comm->nthreads*maxvatom,6,"pair:vatom");
@@ -900,84 +812,72 @@ void PairKIM::set_argument_pointers()
   }
   if (KIM_SupportStatus_Equal(kim_model_support_for_particleVirial,
                               KIM_SUPPORT_STATUS_optional)
-      && (vflag_atom != 1))
-  {
+      && (vflag_atom != 1)) {
     kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(
-        pargs,
-        KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial,
-        reinterpret_cast<double * const>(NULL));
-  }
-  else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial,
-                                      KIM_SUPPORT_STATUS_notSupported))
-  {
+      pargs,
+      KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial,
+      reinterpret_cast<double * const>(NULL));
+  } else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial,
+                                        KIM_SUPPORT_STATUS_notSupported)) {
     kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(
-        pargs, KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, &(vatom[0][0]));
+      pargs, KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial, &(vatom[0][0]));
   }
 
-  if (kimerror)
-  {
-    error->all(FLERR,"Unable to set KIM argument pointers");
-  }
-
-  return;
+  if (kimerror) error->all(FLERR,"Unable to set KIM argument pointers");
 }
 
 /* ---------------------------------------------------------------------- */
 
 void PairKIM::set_lmps_flags()
 {
-   // determint if newton is on or off
-   lmps_using_newton = (force->newton_pair == 1);
+  // determint if newton is on or off
+  lmps_using_newton = (force->newton_pair == 1);
 
-   // determine if running with pair hybrid
-   if (force->pair_match("hybrid",0))
-   {
-     error->all(FLERR,"pair_kim does not support hybrid");
-   }
+  // determine if running with pair hybrid
+  if (force->pair_match("hybrid",0))
+    error->all(FLERR,"pair_kim does not support hybrid");
 
-   // determine unit system and set lmps_units flag
-   if ((strcmp(update->unit_style,"real")==0)) {
-     lmps_units = REAL;
-     lengthUnit = KIM_LENGTH_UNIT_A;
-     energyUnit = KIM_ENERGY_UNIT_kcal_mol;
-     chargeUnit = KIM_CHARGE_UNIT_e;
-     temperatureUnit = KIM_TEMPERATURE_UNIT_K;
-     timeUnit = KIM_TIME_UNIT_fs;
-   } else if ((strcmp(update->unit_style,"metal")==0)) {
-     lmps_units = METAL;
-     lengthUnit = KIM_LENGTH_UNIT_A;
-     energyUnit = KIM_ENERGY_UNIT_eV;
-     chargeUnit = KIM_CHARGE_UNIT_e;
-     temperatureUnit = KIM_TEMPERATURE_UNIT_K;
-     timeUnit = KIM_TIME_UNIT_ps;
-   } else if ((strcmp(update->unit_style,"si")==0)) {
-     lmps_units = SI;
-     lengthUnit = KIM_LENGTH_UNIT_m;
-     energyUnit = KIM_ENERGY_UNIT_J;
-     chargeUnit = KIM_CHARGE_UNIT_C;
-     temperatureUnit = KIM_TEMPERATURE_UNIT_K;
-     timeUnit = KIM_TIME_UNIT_s;
-   } else if ((strcmp(update->unit_style,"cgs")==0)) {
-     lmps_units = CGS;
-     lengthUnit = KIM_LENGTH_UNIT_cm;
-     energyUnit = KIM_ENERGY_UNIT_erg;
-     chargeUnit = KIM_CHARGE_UNIT_statC;
-     temperatureUnit = KIM_TEMPERATURE_UNIT_K;
-     timeUnit = KIM_TIME_UNIT_s;
-   } else if ((strcmp(update->unit_style,"electron")==0)) {
-     lmps_units = ELECTRON;
-     lengthUnit = KIM_LENGTH_UNIT_Bohr;
-     energyUnit = KIM_ENERGY_UNIT_Hartree;
-     chargeUnit = KIM_CHARGE_UNIT_e;
-     temperatureUnit = KIM_TEMPERATURE_UNIT_K;
-     timeUnit = KIM_TIME_UNIT_fs;
-   } else if ((strcmp(update->unit_style,"lj")==0)) {
-     error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models");
-   } else {
-     error->all(FLERR,"Unknown unit_style");
-   }
-
-   return;
+  // determine unit system and set lmps_units flag
+  if ((strcmp(update->unit_style,"real")==0)) {
+    lmps_units = REAL;
+    lengthUnit = KIM_LENGTH_UNIT_A;
+    energyUnit = KIM_ENERGY_UNIT_kcal_mol;
+    chargeUnit = KIM_CHARGE_UNIT_e;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_fs;
+  } else if ((strcmp(update->unit_style,"metal")==0)) {
+    lmps_units = METAL;
+    lengthUnit = KIM_LENGTH_UNIT_A;
+    energyUnit = KIM_ENERGY_UNIT_eV;
+    chargeUnit = KIM_CHARGE_UNIT_e;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_ps;
+  } else if ((strcmp(update->unit_style,"si")==0)) {
+    lmps_units = SI;
+    lengthUnit = KIM_LENGTH_UNIT_m;
+    energyUnit = KIM_ENERGY_UNIT_J;
+    chargeUnit = KIM_CHARGE_UNIT_C;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_s;
+  } else if ((strcmp(update->unit_style,"cgs")==0)) {
+    lmps_units = CGS;
+    lengthUnit = KIM_LENGTH_UNIT_cm;
+    energyUnit = KIM_ENERGY_UNIT_erg;
+    chargeUnit = KIM_CHARGE_UNIT_statC;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_s;
+  } else if ((strcmp(update->unit_style,"electron")==0)) {
+    lmps_units = ELECTRON;
+    lengthUnit = KIM_LENGTH_UNIT_Bohr;
+    energyUnit = KIM_ENERGY_UNIT_Hartree;
+    chargeUnit = KIM_CHARGE_UNIT_e;
+    temperatureUnit = KIM_TEMPERATURE_UNIT_K;
+    timeUnit = KIM_TIME_UNIT_fs;
+  } else if ((strcmp(update->unit_style,"lj")==0)) {
+    error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models");
+  } else {
+    error->all(FLERR,"Unknown unit_style");
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -988,8 +888,7 @@ int PairKIM::check_for_routine_compatibility()
   int numberOfModelRoutineNames;
   KIM_MODEL_ROUTINE_NAME_GetNumberOfModelRoutineNames(
       &numberOfModelRoutineNames);
-  for (int i = 0; i < numberOfModelRoutineNames; ++i)
-  {
+  for (int i = 0; i < numberOfModelRoutineNames; ++i) {
     KIM_ModelRoutineName modelRoutineName;
     KIM_MODEL_ROUTINE_NAME_GetModelRoutineName(i, &modelRoutineName);
 
@@ -997,10 +896,9 @@ int PairKIM::check_for_routine_compatibility()
     int required;
     int error = KIM_Model_IsRoutinePresent(
         pkim, modelRoutineName, &present, &required);
-    if (error) { return true; }
+    if (error) return true;
 
-    if ((present == true) && (required == true))
-    {
+    if ((present == true) && (required == true)) {
       if (!(KIM_ModelRoutineName_Equal(modelRoutineName,
                                        KIM_MODEL_ROUTINE_NAME_Create)
             || KIM_ModelRoutineName_Equal(
@@ -1014,8 +912,9 @@ int PairKIM::check_for_routine_compatibility()
                    modelRoutineName,
                    KIM_MODEL_ROUTINE_NAME_ComputeArgumentsDestroy)
             || KIM_ModelRoutineName_Equal(modelRoutineName,
-                                          KIM_MODEL_ROUTINE_NAME_Destroy)))
-      { return true; }
+                                          KIM_MODEL_ROUTINE_NAME_Destroy))) {
+        return true;
+      }
     }
   }
 
@@ -1030,8 +929,7 @@ void PairKIM::set_kim_model_has_flags()
   int numberOfComputeArgumentNames;
   KIM_COMPUTE_ARGUMENT_NAME_GetNumberOfComputeArgumentNames(
       &numberOfComputeArgumentNames);
-  for (int i = 0; i < numberOfComputeArgumentNames; ++i)
-  {
+  for (int i = 0; i < numberOfComputeArgumentNames; ++i) {
     KIM_ComputeArgumentName computeArgumentName;
     KIM_COMPUTE_ARGUMENT_NAME_GetComputeArgumentName(
         i, &computeArgumentName);
@@ -1040,32 +938,24 @@ void PairKIM::set_kim_model_has_flags()
         pargs, computeArgumentName, &supportStatus);
 
     if (KIM_ComputeArgumentName_Equal(computeArgumentName,
-                                      KIM_COMPUTE_ARGUMENT_NAME_partialEnergy)
-       )
+                                      KIM_COMPUTE_ARGUMENT_NAME_partialEnergy))
       kim_model_support_for_energy = supportStatus;
     else if (KIM_ComputeArgumentName_Equal(
-                 computeArgumentName, KIM_COMPUTE_ARGUMENT_NAME_partialForces)
-            )
+                 computeArgumentName, KIM_COMPUTE_ARGUMENT_NAME_partialForces))
       kim_model_support_for_forces = supportStatus;
-    else if
-        (KIM_ComputeArgumentName_Equal(
-            computeArgumentName,
-            KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy)\
-        )
+    else if (KIM_ComputeArgumentName_Equal(
+               computeArgumentName,
+               KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy))
       kim_model_support_for_particleEnergy = supportStatus;
-    else if
-        (KIM_ComputeArgumentName_Equal(
-            computeArgumentName,
-            KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial)
-        )
+    else if (KIM_ComputeArgumentName_Equal(
+               computeArgumentName,
+               KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial))
       kim_model_support_for_particleVirial = supportStatus;
-    else if (KIM_SupportStatus_Equal(supportStatus, KIM_SUPPORT_STATUS_required)
-            )
-    {
-      std::stringstream msg;
-      msg << "KIM Model requires unsupported compute argument: "
-          << KIM_ComputeArgumentName_ToString(computeArgumentName);
-      error->all(FLERR, msg.str().c_str());
+    else if (KIM_SupportStatus_Equal(supportStatus,
+                                     KIM_SUPPORT_STATUS_required)) {
+      std::string msg("KIM Model requires unsupported compute argument: ");
+      msg += KIM_ComputeArgumentName_ToString(computeArgumentName);
+      error->all(FLERR, msg.c_str());
     }
   }
 
@@ -1092,20 +982,15 @@ void PairKIM::set_kim_model_has_flags()
   int numberOfComputeCallbackNames;
   KIM_COMPUTE_CALLBACK_NAME_GetNumberOfComputeCallbackNames(
       &numberOfComputeCallbackNames);
-  for (int i = 0; i < numberOfComputeCallbackNames; ++i)
-  {
+  for (int i = 0; i < numberOfComputeCallbackNames; ++i) {
     KIM_ComputeCallbackName computeCallbackName;
-    KIM_COMPUTE_CALLBACK_NAME_GetComputeCallbackName(
-        i, &computeCallbackName);
+    KIM_COMPUTE_CALLBACK_NAME_GetComputeCallbackName(i, &computeCallbackName);
     KIM_SupportStatus supportStatus;
-    KIM_ComputeArguments_GetCallbackSupportStatus(
-        pargs, computeCallbackName, &supportStatus);
+    KIM_ComputeArguments_GetCallbackSupportStatus(pargs,
+                                                  computeCallbackName,
+                                                  &supportStatus);
 
     if (KIM_SupportStatus_Equal(supportStatus, KIM_SUPPORT_STATUS_required))
-    {
       error->all(FLERR,"KIM Model requires unsupported compute callback");
-    }
   }
-
-  return;
 }
diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h
index 27bab6c687..aa33b9b271 100644
--- a/src/KIM/pair_kim.h
+++ b/src/KIM/pair_kim.h
@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Contributing authors: Ryan S. Elliott (UMinn)
+   Contributing authors: Ryan S. Elliott (UMinn), Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
@@ -65,108 +65,107 @@ PairStyle(kim,PairKIM)
 // includes from KIM & LAMMPS
 class KIM_API_model;
 #include "pair.h"
+
 extern "C" {
 #include "KIM_SimulatorHeaders.h"
 }
-#include <sstream>
-
 
 namespace LAMMPS_NS {
 
-   class PairKIM : public Pair {
-   public:
-      PairKIM(class LAMMPS*);
-      ~PairKIM();
+class PairKIM : public Pair {
+ public:
+  PairKIM(class LAMMPS*);
+  ~PairKIM();
 
-      // LAMMPS Pair class virtual function prototypes
-      virtual void compute(int, int);
-      virtual void settings(int, char**);
-      virtual void coeff(int, char**);
-      virtual void init_style();
-      virtual void init_list(int id, NeighList *ptr);
-      virtual double init_one(int, int);
-      virtual int pack_reverse_comm(int, int, double*);
-      virtual void unpack_reverse_comm(int, int*, double*);
-      virtual double memory_usage();
+  // LAMMPS Pair class virtual function prototypes
+  virtual void compute(int, int);
+  virtual void settings(int, char**);
+  virtual void coeff(int, char**);
+  virtual void init_style();
+  virtual void init_list(int id, NeighList *ptr);
+  virtual double init_one(int, int);
+  virtual int pack_reverse_comm(int, int, double*);
+  virtual void unpack_reverse_comm(int, int*, double*);
+  virtual double memory_usage();
 
-   protected:
-      // (nearly) all bool flags are not initialized in constructor, but set
-      // explicitly in the indicated function.  All other data members are
-      // initialized in constructor
-      int settings_call_count;
-      int init_style_call_count;
+ protected:
+  // (nearly) all bool flags are not initialized in constructor, but set
+  // explicitly in the indicated function.  All other data members are
+  // initialized in constructor
+  int settings_call_count;
+  int init_style_call_count;
 
-      // values set in settings()
-      char* kim_modelname;
+  // values set in settings()
+  char* kim_modelname;
 
-      // values set in coeff()
+  // values set in coeff()
 
-      // values set in allocate(), called by coeff()
-      virtual void allocate();
-      int* lmps_map_species_to_unique;
+  // values set in allocate(), called by coeff()
+  virtual void allocate();
+  int* lmps_map_species_to_unique;
 
-      // values set in coeff(), after calling allocate()
-      char** lmps_unique_elements;  // names of unique elements given
-                                    // in pair_coeff command
-      int lmps_num_unique_elements;
+  // values set in coeff(), after calling allocate()
+  char** lmps_unique_elements;  // names of unique elements given
+                                // in pair_coeff command
+  int lmps_num_unique_elements;
 
-      // values set in set_lmps_flags(), called from init_style()
-      bool lmps_using_newton;
-      bool lmps_using_molecular;
-      enum unit_sys {REAL, METAL, SI, CGS, ELECTRON};
-      unit_sys lmps_units;
-      KIM_LengthUnit lengthUnit;
-      KIM_EnergyUnit energyUnit;
-      KIM_ChargeUnit chargeUnit;
-      KIM_TemperatureUnit temperatureUnit;
-      KIM_TimeUnit timeUnit;
+  // values set in set_lmps_flags(), called from init_style()
+  bool lmps_using_newton;
+  bool lmps_using_molecular;
+  enum unit_sys {REAL, METAL, SI, CGS, ELECTRON};
+  unit_sys lmps_units;
+  KIM_LengthUnit lengthUnit;
+  KIM_EnergyUnit energyUnit;
+  KIM_ChargeUnit chargeUnit;
+  KIM_TemperatureUnit temperatureUnit;
+  KIM_TimeUnit timeUnit;
 
-      KIM_Model * pkim;
-      KIM_ComputeArguments * pargs;
+  KIM_Model * pkim;
+  KIM_ComputeArguments * pargs;
 
-      // values set in set_kim_model_has_flags(), called by kim_init()
-      KIM_SupportStatus kim_model_support_for_energy;
-      KIM_SupportStatus kim_model_support_for_forces;
-      KIM_SupportStatus kim_model_support_for_particleEnergy;
-      KIM_SupportStatus kim_model_support_for_particleVirial;
+  // values set in set_kim_model_has_flags(), called by kim_init()
+  KIM_SupportStatus kim_model_support_for_energy;
+  KIM_SupportStatus kim_model_support_for_forces;
+  KIM_SupportStatus kim_model_support_for_particleEnergy;
+  KIM_SupportStatus kim_model_support_for_particleVirial;
 
-      // values set in kim_init()
-      bool kim_init_ok;
-      int lmps_local_tot_num_atoms;
-      double kim_global_influence_distance;  // KIM Model cutoff value
-      int kim_number_of_neighbor_lists;
-      double const * kim_cutoff_values;
-      int const * modelWillNotRequestNeighborsOfNoncontributingParticles;
-       class NeighList ** neighborLists;
+  // values set in kim_init()
+  bool kim_init_ok;
+  int lmps_local_tot_num_atoms;
+  double kim_global_influence_distance;  // KIM Model cutoff value
+  int kim_number_of_neighbor_lists;
+  double const * kim_cutoff_values;
+  int const * modelWillNotRequestNeighborsOfNoncontributingParticles;
+  class NeighList ** neighborLists;
 
-      // values set in init_style()
-      bool kim_particle_codes_ok;
-      int *kim_particle_codes;
+  // values set in init_style()
+  bool kim_particle_codes_ok;
+  int *kim_particle_codes;
 
-      // values set in compute()
-      int lmps_maxalloc;              // max allocated memory value
-      int* kim_particleSpecies;       // array of KIM particle species
-      int* kim_particleContributing;  // array of KIM particle contributing
-      int* lmps_stripped_neigh_list;  // neighbors of one atom, used when LAMMPS
-                                      // is in molecular mode
-      int** lmps_stripped_neigh_ptr;  // pointer into lists
+  // values set in compute()
+  int lmps_maxalloc;              // max allocated memory value
+  int* kim_particleSpecies;       // array of KIM particle species
+  int* kim_particleContributing;  // array of KIM particle contributing
+  int* lmps_stripped_neigh_list;  // neighbors of one atom, used when LAMMPS
+                                  // is in molecular mode
+  int** lmps_stripped_neigh_ptr;  // pointer into lists
 
-      // KIM specific helper functions
-      virtual void set_contributing();
-      virtual void kim_init();
-      virtual void kim_free();
-      virtual void set_argument_pointers();
-      virtual void set_lmps_flags();
-      virtual void set_kim_model_has_flags();
-      virtual int check_for_routine_compatibility();
-      // static methods used as callbacks from KIM
-      static int get_neigh(
-         void const * const dataObject,
-         int const numberOfCutoffs, double const * const cutoffs,
-         int const neighborListIndex, int const particleNumber,
-         int * const numberOfNeighbors,
-         int const ** const neighborsOfParticle);
-   };
+  // KIM specific helper functions
+  virtual void set_contributing();
+  virtual void kim_init();
+  virtual void kim_free();
+  virtual void set_argument_pointers();
+  virtual void set_lmps_flags();
+  virtual void set_kim_model_has_flags();
+  virtual int check_for_routine_compatibility();
+  // static methods used as callbacks from KIM
+  static int get_neigh(
+    void const * const dataObject,
+    int const numberOfCutoffs, double const * const cutoffs,
+    int const neighborListIndex, int const particleNumber,
+    int * const numberOfNeighbors,
+    int const ** const neighborsOfParticle);
+};
 }
 
 #endif
@@ -184,7 +183,10 @@ The KIM model was unable, for some reason, to complete the computation.
 
 E: 'KIMvirial' or 'LAMMPSvirial' not supported with kim-api.
 
-"KIMvirial or "LAMMPSvirial" found on the pair_style line.  These keys are not supported kim-api. (The virial computation is always performed by LAMMPS.) Please remove these keys, make sure the KIM model you are using supports kim-api, and rerun.
+"KIMvirial or "LAMMPSvirial" found on the pair_style line.  These keys
+are not supported kim-api.  (The virial computation is always performed
+by LAMMPS.) Please remove these keys, make sure the KIM model you are
+using supports kim-api, and rerun.
 
 E: Illegal pair_style command
 
diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh
index 941cecad9b..460750ec43 100755
--- a/src/KOKKOS/Install.sh
+++ b/src/KOKKOS/Install.sh
@@ -110,6 +110,8 @@ action fix_gravity_kokkos.cpp
 action fix_gravity_kokkos.h
 action fix_langevin_kokkos.cpp
 action fix_langevin_kokkos.h
+action fix_minimize_kokkos.cpp
+action fix_minimize_kokkos.h
 action fix_neigh_history_kokkos.cpp
 action fix_neigh_history_kokkos.h
 action fix_nh_kokkos.cpp
@@ -183,6 +185,12 @@ action nbin_ssa_kokkos.cpp nbin_ssa.cpp
 action nbin_ssa_kokkos.h nbin_ssa.h
 action math_special_kokkos.cpp
 action math_special_kokkos.h
+action min_cg_kokkos.cpp
+action min_cg_kokkos.h
+action min_kokkos.cpp
+action min_kokkos.h
+action min_linesearch_kokkos.cpp
+action min_linesearch_kokkos.h
 action pack_kokkos.h pack.h
 action pair_buck_coul_cut_kokkos.cpp
 action pair_buck_coul_cut_kokkos.h
diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp
index 0f46c958d6..fd9757aab3 100644
--- a/src/KOKKOS/angle_charmm_kokkos.cpp
+++ b/src/KOKKOS/angle_charmm_kokkos.cpp
@@ -15,9 +15,9 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "angle_charmm_kokkos.h"
 #include <cmath>
 #include <cstdlib>
-#include "angle_charmm_kokkos.h"
 #include "atom_kokkos.h"
 #include "neighbor_kokkos.h"
 #include "domain.h"
diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp
index 836714764d..809ce7e7dd 100644
--- a/src/KOKKOS/angle_class2_kokkos.cpp
+++ b/src/KOKKOS/angle_class2_kokkos.cpp
@@ -15,9 +15,9 @@
    Contributing author: Ray Shan (Materials Design)
 ------------------------------------------------------------------------- */
 
+#include "angle_class2_kokkos.h"
 #include <cmath>
 #include <cstdlib>
-#include "angle_class2_kokkos.h"
 #include "atom_kokkos.h"
 #include "neighbor_kokkos.h"
 #include "domain.h"
diff --git a/src/KOKKOS/angle_cosine_kokkos.cpp b/src/KOKKOS/angle_cosine_kokkos.cpp
index 4a4866948f..da0ff398f1 100644
--- a/src/KOKKOS/angle_cosine_kokkos.cpp
+++ b/src/KOKKOS/angle_cosine_kokkos.cpp
@@ -15,9 +15,9 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "angle_cosine_kokkos.h"
 #include <cmath>
 #include <cstdlib>
-#include "angle_cosine_kokkos.h"
 #include "atom_kokkos.h"
 #include "neighbor_kokkos.h"
 #include "domain.h"
diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp
index dbe705800c..fc274bb894 100644
--- a/src/KOKKOS/angle_harmonic_kokkos.cpp
+++ b/src/KOKKOS/angle_harmonic_kokkos.cpp
@@ -15,9 +15,9 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "angle_harmonic_kokkos.h"
 #include <cmath>
 #include <cstdlib>
-#include "angle_harmonic_kokkos.h"
 #include "atom_kokkos.h"
 #include "neighbor_kokkos.h"
 #include "domain.h"
diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp
index 813c5ddbf2..4637a9a21c 100644
--- a/src/KOKKOS/atom_kokkos.cpp
+++ b/src/KOKKOS/atom_kokkos.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "atom_kokkos.h"
+#include <mpi.h>
 #include "atom_vec.h"
 #include "atom_vec_kokkos.h"
 #include "comm_kokkos.h"
diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp
index 06358289b6..736e1c1fca 100644
--- a/src/KOKKOS/atom_vec_angle_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_angle_kokkos.h"
 #include "atom_kokkos.h"
 #include "comm_kokkos.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "atom_masks.h"
diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp
index 6e530bdbe9..4fec5740d6 100644
--- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_atomic_kokkos.h"
 #include "atom_kokkos.h"
 #include "comm_kokkos.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "atom_masks.h"
diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp
index 3195ea0876..74c05a506c 100644
--- a/src/KOKKOS/atom_vec_bond_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_bond_kokkos.h"
 #include "atom_kokkos.h"
 #include "comm_kokkos.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "atom_masks.h"
diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp
index 77d0c1dae3..3f26b1e9ea 100644
--- a/src/KOKKOS/atom_vec_charge_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_charge_kokkos.h"
 #include "atom_kokkos.h"
 #include "comm_kokkos.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "atom_masks.h"
diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp
index 317914e4f8..144ef26f19 100644
--- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_dpd_kokkos.h"
 #include "atom_kokkos.h"
 #include "comm_kokkos.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "atom_masks.h"
diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp
index 19443b231f..1fdbcbec8c 100644
--- a/src/KOKKOS/atom_vec_full_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_full_kokkos.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_full_kokkos.h"
 #include "atom_kokkos.h"
 #include "comm_kokkos.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "atom_masks.h"
diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp
index c4dd90ce05..40303051b2 100644
--- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "atom_vec_hybrid_kokkos.h"
+#include <cstring>
 #include "atom_kokkos.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "memory_kokkos.h"
diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.h b/src/KOKKOS/atom_vec_hybrid_kokkos.h
index 1bbbd26319..4cfb186b17 100644
--- a/src/KOKKOS/atom_vec_hybrid_kokkos.h
+++ b/src/KOKKOS/atom_vec_hybrid_kokkos.h
@@ -20,7 +20,6 @@ AtomStyle(hybrid/kk,AtomVecHybridKokkos)
 #ifndef LMP_ATOM_VEC_HYBRID_KOKKOS_H
 #define LMP_ATOM_VEC_HYBRID_KOKKOS_H
 
-#include <cstdio>
 #include "atom_vec_kokkos.h"
 #include "kokkos_type.h"
 
diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp
index 9871b1247a..f3b4ae98ca 100644
--- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp
@@ -11,14 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_molecular_kokkos.h"
 #include "atom_kokkos.h"
 #include "comm_kokkos.h"
 #include "domain.h"
 #include "modify.h"
 #include "fix.h"
-#include "force.h"
 #include "atom_masks.h"
 #include "memory_kokkos.h"
 #include "error.h"
diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp
index 3b64ceeb42..7e217df2a6 100644
--- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp
@@ -11,16 +11,14 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "atom_vec_sphere_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "atom_kokkos.h"
 #include "atom_masks.h"
 #include "comm_kokkos.h"
 #include "domain.h"
 #include "modify.h"
-#include "force.h"
 #include "fix.h"
 #include "fix_adapt.h"
 #include "math_const.h"
diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp
index 798fb41c92..04281bfdd2 100644
--- a/src/KOKKOS/bond_class2_kokkos.cpp
+++ b/src/KOKKOS/bond_class2_kokkos.cpp
@@ -15,9 +15,9 @@
    Contributing author: Ray Shan (Materials Design)
 ------------------------------------------------------------------------- */
 
+#include "bond_class2_kokkos.h"
 #include <cmath>
 #include <cstdlib>
-#include "bond_class2_kokkos.h"
 #include "atom_kokkos.h"
 #include "neighbor_kokkos.h"
 #include "domain.h"
diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp
index b5cdc1a05a..361bb61f7e 100644
--- a/src/KOKKOS/bond_fene_kokkos.cpp
+++ b/src/KOKKOS/bond_fene_kokkos.cpp
@@ -15,9 +15,9 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "bond_fene_kokkos.h"
 #include <cmath>
 #include <cstdlib>
-#include "bond_fene_kokkos.h"
 #include "atom_kokkos.h"
 #include "neighbor_kokkos.h"
 #include "domain.h"
diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp
index 51a9fa4389..792d98fe88 100644
--- a/src/KOKKOS/bond_harmonic_kokkos.cpp
+++ b/src/KOKKOS/bond_harmonic_kokkos.cpp
@@ -15,9 +15,9 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "bond_harmonic_kokkos.h"
 #include <cmath>
 #include <cstdlib>
-#include "bond_harmonic_kokkos.h"
 #include "atom_kokkos.h"
 #include "neighbor_kokkos.h"
 #include "domain.h"
diff --git a/src/KOKKOS/comm_tiled_kokkos.cpp b/src/KOKKOS/comm_tiled_kokkos.cpp
index 81cf1f0563..fc6de0a0d7 100644
--- a/src/KOKKOS/comm_tiled_kokkos.cpp
+++ b/src/KOKKOS/comm_tiled_kokkos.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "comm_tiled_kokkos.h"
+#include <cstring>
 #include "comm_brick.h"
 #include "atom_kokkos.h"
 #include "atom_vec.h"
diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp
index 7b76f54f57..a2fcf63125 100644
--- a/src/KOKKOS/compute_temp_kokkos.cpp
+++ b/src/KOKKOS/compute_temp_kokkos.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_temp_kokkos.h"
 #include <mpi.h>
 #include <cstring>
-#include "compute_temp_kokkos.h"
 #include "atom_kokkos.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp
index 61ddcc425a..94fd0b9bb7 100644
--- a/src/KOKKOS/dihedral_charmm_kokkos.cpp
+++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp
@@ -15,9 +15,9 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "dihedral_charmm_kokkos.h"
 #include <cmath>
 #include <cstdlib>
-#include "dihedral_charmm_kokkos.h"
 #include "atom_kokkos.h"
 #include "comm.h"
 #include "neighbor_kokkos.h"
diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp
index 98436bc696..4b8d171f61 100644
--- a/src/KOKKOS/dihedral_class2_kokkos.cpp
+++ b/src/KOKKOS/dihedral_class2_kokkos.cpp
@@ -15,9 +15,9 @@
    Contributing author: Ray Shan (Materials Design)
 ------------------------------------------------------------------------- */
 
+#include "dihedral_class2_kokkos.h"
 #include <cmath>
 #include <cstdlib>
-#include "dihedral_class2_kokkos.h"
 #include "atom_kokkos.h"
 #include "comm.h"
 #include "neighbor_kokkos.h"
diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp
index f50dea2c36..825d106e04 100644
--- a/src/KOKKOS/dihedral_opls_kokkos.cpp
+++ b/src/KOKKOS/dihedral_opls_kokkos.cpp
@@ -15,9 +15,9 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "dihedral_opls_kokkos.h"
 #include <cmath>
 #include <cstdlib>
-#include "dihedral_opls_kokkos.h"
 #include "atom_kokkos.h"
 #include "comm.h"
 #include "neighbor_kokkos.h"
diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp
index 7b9336ed3b..05eb1c22f6 100644
--- a/src/KOKKOS/fix_deform_kokkos.cpp
+++ b/src/KOKKOS/fix_deform_kokkos.cpp
@@ -15,10 +15,10 @@
    Contributing author: Pieter in 't Veld (SNL)
 ------------------------------------------------------------------------- */
 
+#include "fix_deform_kokkos.h"
 #include <cstring>
 #include <cstdlib>
 #include <cmath>
-#include "fix_deform_kokkos.h"
 #include "atom_kokkos.h"
 #include "update.h"
 #include "comm.h"
diff --git a/src/KOKKOS/fix_dpd_energy_kokkos.cpp b/src/KOKKOS/fix_dpd_energy_kokkos.cpp
index d092cb4802..20579a6dc5 100644
--- a/src/KOKKOS/fix_dpd_energy_kokkos.cpp
+++ b/src/KOKKOS/fix_dpd_energy_kokkos.cpp
@@ -11,15 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
 #include "fix_dpd_energy_kokkos.h"
 #include "atom_masks.h"
 #include "atom_kokkos.h"
-#include "force.h"
 #include "update.h"
-#include "respa.h"
-#include "modify.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/KOKKOS/fix_enforce2d_kokkos.cpp b/src/KOKKOS/fix_enforce2d_kokkos.cpp
index 346e440f55..bf2a882539 100644
--- a/src/KOKKOS/fix_enforce2d_kokkos.cpp
+++ b/src/KOKKOS/fix_enforce2d_kokkos.cpp
@@ -15,11 +15,11 @@
    Contributing authors: Stefan Paquay & Matthew Peterson (Brandeis University)
 ------------------------------------------------------------------------- */
 
+#include "fix_enforce2d_kokkos.h"
 #include "atom_masks.h"
 #include "atom_kokkos.h"
 #include "comm.h"
 #include "error.h"
-#include "fix_enforce2d_kokkos.h"
 
 
 using namespace LAMMPS_NS;
diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp
index 2f730d1193..89561c9a92 100644
--- a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp
+++ b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp
@@ -15,8 +15,6 @@
    Contributing author: Stan Moore (Sandia)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_eos_table_rx_kokkos.h"
 #include "atom_kokkos.h"
 #include "error.h"
@@ -24,7 +22,6 @@
 #include "memory_kokkos.h"
 #include "comm.h"
 #include <cmath>
-#include "modify.h"
 #include "atom_masks.h"
 
 #define MAXLINE 1024
diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp
index 0947fee693..651f790a25 100644
--- a/src/KOKKOS/fix_langevin_kokkos.cpp
+++ b/src/KOKKOS/fix_langevin_kokkos.cpp
@@ -11,23 +11,20 @@
    See the README file in the top-level LAMMPS directory.
    ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_langevin_kokkos.h"
+#include <cmath>
 #include "atom_masks.h"
 #include "atom_kokkos.h"
 #include "force.h"
+#include "group.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
 #include "memory_kokkos.h"
-#include "group.h"
-#include "random_mars.h"
 #include "compute.h"
 #include "comm.h"
 #include "modify.h"
 #include "input.h"
+#include "region.h"
 #include "variable.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/KOKKOS/fix_minimize_kokkos.cpp b/src/KOKKOS/fix_minimize_kokkos.cpp
new file mode 100644
index 0000000000..e7b10dbb8e
--- /dev/null
+++ b/src/KOKKOS/fix_minimize_kokkos.cpp
@@ -0,0 +1,257 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "fix_minimize_kokkos.h"
+#include "atom_kokkos.h"
+#include "domain.h"
+#include "memory_kokkos.h"
+#include "atom_masks.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ---------------------------------------------------------------------- */
+
+FixMinimizeKokkos::FixMinimizeKokkos(LAMMPS *lmp, int narg, char **arg) :
+  FixMinimize(lmp, narg, arg)
+{
+  atomKK = (AtomKokkos *) atom;
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixMinimizeKokkos::~FixMinimizeKokkos()
+{
+  memoryKK->destroy_kokkos(k_vectors,vectors);
+  vectors = NULL;
+}
+
+/* ----------------------------------------------------------------------
+   allocate/initialize memory for a new vector with 3 elements per atom
+------------------------------------------------------------------------- */
+
+void FixMinimizeKokkos::add_vector_kokkos()
+{
+  int n = 3;
+
+  memory->grow(peratom,nvector+1,"minimize:peratom");
+  peratom[nvector] = n;
+
+  // d_vectors needs to be LayoutRight for subviews
+
+  k_vectors.sync<LMPDeviceType>();
+
+  memoryKK->grow_kokkos(k_vectors,vectors,nvector+1,atom->nmax*n,
+                      "minimize:vectors");
+  d_vectors = k_vectors.d_view;
+  h_vectors = k_vectors.h_view;
+
+  k_vectors.modify<LMPDeviceType>();
+
+  nvector++;
+}
+
+/* ----------------------------------------------------------------------
+   return a pointer to the Mth vector
+------------------------------------------------------------------------- */
+
+DAT::t_ffloat_1d FixMinimizeKokkos::request_vector_kokkos(int m)
+{
+  k_vectors.sync<LMPDeviceType>();
+
+  return Kokkos::subview(d_vectors,m,Kokkos::ALL);
+}
+
+/* ----------------------------------------------------------------------
+   reset x0 for atoms that moved across PBC via reneighboring in line search
+   x0 = 1st vector
+   must do minimum_image using original box stored at beginning of line search
+   swap & set_global_box() change to original box, then restore current box
+------------------------------------------------------------------------- */
+
+void FixMinimizeKokkos::reset_coords()
+{
+  box_swap();
+  domain->set_global_box();
+
+  int nlocal = atom->nlocal;
+
+  atomKK->sync(Device,X_MASK);
+  k_vectors.sync<LMPDeviceType>();
+
+  {
+    // local variables for lambda capture
+
+    auto triclinic = domain->triclinic;
+    auto xperiodic = domain->xperiodic;
+    auto xprd_half = domain->xprd_half;
+    auto xprd = domain->xprd;
+    auto yperiodic = domain->yperiodic;
+    auto yprd_half = domain->yprd_half;
+    auto yprd = domain->yprd;
+    auto zperiodic = domain->zperiodic;
+    auto zprd_half = domain->zprd_half;
+    auto zprd = domain->zprd;
+    auto xy = domain->xy;
+    auto xz = domain->xz;
+    auto yz = domain->yz;
+    auto l_x = atomKK->k_x.d_view;
+    auto l_x0 = Kokkos::subview(d_vectors,0,Kokkos::ALL);
+
+    Kokkos::parallel_for(nlocal, LAMMPS_LAMBDA(const int& i) {
+      const int n = i*3;
+      double dx0 = l_x(i,0) - l_x0[n];
+      double dy0 = l_x(i,1) - l_x0[n+1];
+      double dz0 = l_x(i,2) - l_x0[n+2];
+      double dx = dx0;
+      double dy = dy0;
+      double dz = dz0;
+      // domain->minimum_image(dx,dy,dz);
+      {
+        if (triclinic == 0) {
+          if (xperiodic) {
+            if (fabs(dx) > xprd_half) {
+              if (dx < 0.0) dx += xprd;
+              else dx -= xprd;
+            }
+          }
+          if (yperiodic) {
+            if (fabs(dy) > yprd_half) {
+              if (dy < 0.0) dy += yprd;
+              else dy -= yprd;
+            }
+          }
+          if (zperiodic) {
+            if (fabs(dz) > zprd_half) {
+              if (dz < 0.0) dz += zprd;
+              else dz -= zprd;
+            }
+          }
+
+        } else {
+          if (zperiodic) {
+            if (fabs(dz) > zprd_half) {
+              if (dz < 0.0) {
+                dz += zprd;
+                dy += yz;
+                dx += xz;
+              } else {
+                dz -= zprd;
+                dy -= yz;
+                dx -= xz;
+              }
+            }
+          }
+          if (yperiodic) {
+            if (fabs(dy) > yprd_half) {
+              if (dy < 0.0) {
+                dy += yprd;
+                dx += xy;
+              } else {
+                dy -= yprd;
+                dx -= xy;
+              }
+            }
+          }
+          if (xperiodic) {
+            if (fabs(dx) > xprd_half) {
+              if (dx < 0.0) dx += xprd;
+              else dx -= xprd;
+            }
+          }
+        }
+      } // end domain->minimum_image(dx,dy,dz);
+      if (dx != dx0) l_x0[n] = l_x(i,0) - dx;
+      if (dy != dy0) l_x0[n+1] = l_x(i,1) - dy;
+      if (dz != dz0) l_x0[n+2] = l_x(i,2) - dz;
+    });
+  }
+  k_vectors.modify<LMPDeviceType>();
+
+  box_swap();
+  domain->set_global_box();
+}
+
+/* ----------------------------------------------------------------------
+   allocate local atom-based arrays
+------------------------------------------------------------------------- */
+
+void FixMinimizeKokkos::grow_arrays(int nmax)
+{
+  k_vectors.sync<LMPDeviceType>();
+  memoryKK->grow_kokkos(k_vectors,vectors,nvector,3*nmax,"minimize:vector");
+  d_vectors = k_vectors.d_view;
+  h_vectors = k_vectors.h_view;
+  k_vectors.modify<LMPDeviceType>();
+}
+
+/* ----------------------------------------------------------------------
+   copy values within local atom-based arrays
+------------------------------------------------------------------------- */
+
+void FixMinimizeKokkos::copy_arrays(int i, int j, int /*delflag*/)
+{
+  int m,iper,nper,ni,nj;
+
+  k_vectors.sync<LMPHostType>();
+
+  for (m = 0; m < nvector; m++) {
+    nper = 3;
+    ni = nper*i;
+    nj = nper*j;
+    for (iper = 0; iper < nper; iper++) h_vectors(m,nj++) = h_vectors(m,ni++);
+  }
+
+  k_vectors.modify<LMPHostType>();
+}
+
+/* ----------------------------------------------------------------------
+   pack values in local atom-based arrays for exchange with another proc
+------------------------------------------------------------------------- */
+
+int FixMinimizeKokkos::pack_exchange(int i, double *buf)
+{
+  int m,iper,nper,ni;
+
+  k_vectors.sync<LMPHostType>();
+
+  int n = 0;
+  for (m = 0; m < nvector; m++) {
+    nper = peratom[m];
+    ni = nper*i;
+    for (iper = 0; iper < nper; iper++) buf[n++] = h_vectors(m,ni++);
+  }
+  return n;
+}
+
+/* ----------------------------------------------------------------------
+   unpack values in local atom-based arrays from exchange with another proc
+------------------------------------------------------------------------- */
+
+int FixMinimizeKokkos::unpack_exchange(int nlocal, double *buf)
+{
+  int m,iper,nper,ni;
+
+  k_vectors.sync<LMPHostType>();
+
+  int n = 0;
+  for (m = 0; m < nvector; m++) {
+    nper = peratom[m];
+    ni = nper*nlocal;
+    for (iper = 0; iper < nper; iper++) h_vectors(m,ni++) = buf[n++];
+  }
+
+  k_vectors.modify<LMPHostType>();
+
+  return n;
+}
diff --git a/src/KOKKOS/fix_minimize_kokkos.h b/src/KOKKOS/fix_minimize_kokkos.h
new file mode 100644
index 0000000000..921cb2fc5d
--- /dev/null
+++ b/src/KOKKOS/fix_minimize_kokkos.h
@@ -0,0 +1,58 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(MINIMIZE/kk,FixMinimizeKokkos)
+FixStyle(MINIMIZE/kk/device,FixMinimizeKokkos)
+FixStyle(MINIMIZE/kk/host,FixMinimizeKokkos)
+
+#else
+
+#ifndef LMP_FIX_MINIMIZE_KOKKOS_H
+#define LMP_FIX_MINIMIZE_KOKKOS_H
+
+#include "fix_minimize.h"
+#include "kokkos_type.h"
+
+namespace LAMMPS_NS {
+
+class FixMinimizeKokkos : public FixMinimize {
+  friend class MinLineSearchKokkos;
+
+ public:
+  FixMinimizeKokkos(class LAMMPS *, int, char **);
+  virtual ~FixMinimizeKokkos();
+  void init() {}
+
+  void grow_arrays(int);
+  void copy_arrays(int, int, int);
+  int pack_exchange(int, double *);
+  int unpack_exchange(int, double *);
+
+  void add_vector_kokkos();
+  DAT::t_float_1d request_vector_kokkos(int);
+  void reset_coords();
+
+  DAT::tdual_float_2d k_vectors;
+  DAT::t_float_2d d_vectors;
+  HAT::t_float_2d h_vectors;
+};
+
+}
+
+#endif
+#endif
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp
index 38500531ca..2d4911bfda 100644
--- a/src/KOKKOS/fix_momentum_kokkos.cpp
+++ b/src/KOKKOS/fix_momentum_kokkos.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_momentum_kokkos.h"
 #include <cstdlib>
 #include <cstring>
-#include "fix_momentum_kokkos.h"
 #include "atom_kokkos.h"
 #include "atom_masks.h"
 #include "domain.h"
diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp
index 5f53950fe6..8cfe7111dd 100644
--- a/src/KOKKOS/fix_neigh_history_kokkos.cpp
+++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp
@@ -99,7 +99,7 @@ void FixNeighHistoryKokkos<DeviceType>::pre_exchange()
 
   copymode = 0;
 
-  comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
+  maxexchange = (dnum+1)*maxpartner+1;
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp
index fae9ef8f30..578f2f5c70 100644
--- a/src/KOKKOS/fix_nh_kokkos.cpp
+++ b/src/KOKKOS/fix_nh_kokkos.cpp
@@ -15,10 +15,10 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "fix_nh_kokkos.h"
 #include <cstring>
 #include <cstdlib>
 #include <cmath>
-#include "fix_nh_kokkos.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "force.h"
diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp
index c5072e6ae9..3830860fd7 100644
--- a/src/KOKKOS/fix_nph_kokkos.cpp
+++ b/src/KOKKOS/fix_nph_kokkos.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nph_kokkos.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp
index c488c8e4f3..5b751c9e4d 100644
--- a/src/KOKKOS/fix_npt_kokkos.cpp
+++ b/src/KOKKOS/fix_npt_kokkos.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_npt_kokkos.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp
index ca7f728370..f94b68dbce 100644
--- a/src/KOKKOS/fix_nve_kokkos.cpp
+++ b/src/KOKKOS/fix_nve_kokkos.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_nve_kokkos.h"
 #include <cstdio>
 #include <cstring>
-#include "fix_nve_kokkos.h"
 #include "atom_masks.h"
 #include "atom_kokkos.h"
 #include "force.h"
diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp
index 4db42a62fb..66165dd7bc 100644
--- a/src/KOKKOS/fix_nvt_kokkos.cpp
+++ b/src/KOKKOS/fix_nvt_kokkos.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nvt_kokkos.h"
+#include <cstring>
 #include "group.h"
 #include "modify.h"
 #include "error.h"
diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp
index 6860676911..ff374b885f 100644
--- a/src/KOKKOS/fix_property_atom_kokkos.cpp
+++ b/src/KOKKOS/fix_property_atom_kokkos.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_property_atom_kokkos.h"
 #include <cstdlib>
 #include <cstring>
-#include "fix_property_atom_kokkos.h"
 #include "atom_kokkos.h"
 #include "comm.h"
 #include "memory_kokkos.h"
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index 12369261b3..e51fbacaaf 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -16,26 +16,19 @@
                           Kamesh Arumugam (NVIDIA)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "fix_qeq_reax_kokkos.h"
+#include <cmath>
 #include "kokkos.h"
 #include "atom.h"
 #include "atom_masks.h"
 #include "atom_kokkos.h"
 #include "comm.h"
 #include "force.h"
-#include "group.h"
-#include "modify.h"
 #include "neighbor.h"
 #include "neigh_list_kokkos.h"
 #include "neigh_request.h"
 #include "update.h"
 #include "integrate.h"
-#include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "pair_reaxc_kokkos.h"
diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp
index 9aed0b9ae4..51702bc603 100644
--- a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp
+++ b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp
@@ -15,26 +15,13 @@
    Contributing author: Stan Moore (Sandia)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
-#include "fix_ave_atom.h"
 #include "fix_reaxc_bonds_kokkos.h"
 #include "atom.h"
-#include "update.h"
 #include "pair_reaxc_kokkos.h"
-#include "modify.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "comm.h"
 #include "force.h"
 #include "compute.h"
-#include "input.h"
-#include "variable.h"
 #include "memory_kokkos.h"
 #include "error.h"
-#include "reaxc_list.h"
-#include "reaxc_types.h"
 #include "reaxc_defs.h"
 #include "atom_masks.h"
 
diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.cpp b/src/KOKKOS/fix_reaxc_species_kokkos.cpp
index bd92251960..f3bce2f9c0 100644
--- a/src/KOKKOS/fix_reaxc_species_kokkos.cpp
+++ b/src/KOKKOS/fix_reaxc_species_kokkos.cpp
@@ -15,27 +15,18 @@
    Contributing authors: Stan Moore (Sandia)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cmath>
-#include "atom.h"
-#include <cstring>
-#include "fix_ave_atom.h"
 #include "fix_reaxc_species_kokkos.h"
-#include "domain.h"
-#include "update.h"
+#include "atom.h"
+#include "fix_ave_atom.h"
+#include "reaxc_defs.h"
 #include "pair_reaxc_kokkos.h"
-#include "modify.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "comm.h"
 #include "force.h"
-#include "compute.h"
 #include "input.h"
-#include "variable.h"
 #include "memory_kokkos.h"
 #include "error.h"
-#include "reaxc_list.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp
index 80333e1e9b..e06fc14585 100644
--- a/src/KOKKOS/fix_rx_kokkos.cpp
+++ b/src/KOKKOS/fix_rx_kokkos.cpp
@@ -11,15 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
 #include "fix_rx_kokkos.h"
+#include <cstring>
 #include "atom_masks.h"
 #include "atom_kokkos.h"
 #include "force.h"
 #include "memory_kokkos.h"
 #include "update.h"
-#include "respa.h"
 #include "modify.h"
 #include "neighbor.h"
 #include "neigh_list_kokkos.h"
diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp
index 634bc05ac3..6f14a71382 100644
--- a/src/KOKKOS/fix_setforce_kokkos.cpp
+++ b/src/KOKKOS/fix_setforce_kokkos.cpp
@@ -11,22 +11,20 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "fix_setforce_kokkos.h"
+#include <cstring>
 #include "atom_kokkos.h"
 #include "update.h"
 #include "modify.h"
 #include "domain.h"
 #include "region.h"
-#include "respa.h"
 #include "input.h"
 #include "variable.h"
 #include "memory_kokkos.h"
 #include "error.h"
-#include "force.h"
 #include "atom_masks.h"
 #include "kokkos_base.h"
+#include "region.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/KOKKOS/fix_setforce_kokkos.h b/src/KOKKOS/fix_setforce_kokkos.h
index 3cbf3d3720..ecbfd71e36 100644
--- a/src/KOKKOS/fix_setforce_kokkos.h
+++ b/src/KOKKOS/fix_setforce_kokkos.h
@@ -23,7 +23,6 @@ FixStyle(setforce/kk/host,FixSetForceKokkos<LMPHostType>)
 #define LMP_FIX_SET_FORCE_KOKKOS_H
 
 #include "fix_setforce.h"
-#include "region.h"
 #include "kokkos_type.h"
 
 namespace LAMMPS_NS {
@@ -82,7 +81,7 @@ class FixSetForceKokkos : public FixSetForce {
   typename AT::t_f_array f;
   typename AT::t_int_1d_randomread mask;
 
-  Region* region;
+  class Region* region;
 };
 
 }
diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp
index 968f877abd..9bd8594341 100644
--- a/src/KOKKOS/fix_shardlow_kokkos.cpp
+++ b/src/KOKKOS/fix_shardlow_kokkos.cpp
@@ -33,31 +33,23 @@
    135, 204105.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "fix_shardlow_kokkos.h"
+#include <cmath>
+#include <cstdlib>
 #include "atom.h"
 #include "atom_masks.h"
 #include "atom_kokkos.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
-#include <cmath>
-#include "atom_vec.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list_kokkos.h"
 #include "neigh_request.h"
 #include "memory_kokkos.h"
 #include "domain.h"
-#include "modify.h"
-// #include "pair_dpd_fdt.h"
 #include "pair_dpd_fdt_energy_kokkos.h"
-#include "pair.h"
 #include "npair_ssa_kokkos.h"
-#include "citeme.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/KOKKOS/fix_wall_lj93_kokkos.cpp b/src/KOKKOS/fix_wall_lj93_kokkos.cpp
index 5dbb054175..61346144c8 100644
--- a/src/KOKKOS/fix_wall_lj93_kokkos.cpp
+++ b/src/KOKKOS/fix_wall_lj93_kokkos.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "fix_wall_lj93_kokkos.h"
+#include <cmath>
 #include "atom_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp
index 75a5c1a81e..ba104d19a9 100644
--- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp
+++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_wall_reflect_kokkos.h"
 #include <cstdlib>
 #include <cstring>
-#include "fix_wall_reflect_kokkos.h"
 #include "atom_kokkos.h"
 #include "comm.h"
 #include "update.h"
diff --git a/src/KOKKOS/gridcomm_kokkos.cpp b/src/KOKKOS/gridcomm_kokkos.cpp
index 348217634b..ac33b15d73 100644
--- a/src/KOKKOS/gridcomm_kokkos.cpp
+++ b/src/KOKKOS/gridcomm_kokkos.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "gridcomm_kokkos.h"
+#include <mpi.h>
 #include "comm.h"
 #include "kspace.h"
 #include "memory_kokkos.h"
diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp
index ad32e6da4e..defd5e16f5 100644
--- a/src/KOKKOS/improper_class2_kokkos.cpp
+++ b/src/KOKKOS/improper_class2_kokkos.cpp
@@ -15,23 +15,16 @@
    Contributing author: Ray Shan (Materials Design)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cmath>
-#include <cstdlib>
 #include "improper_class2_kokkos.h"
+#include <cmath>
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "neighbor_kokkos.h"
-#include "domain.h"
 #include "force.h"
-#include "update.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define TOLERANCE 0.05
 #define SMALL     0.001
diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp
index bb397a2c2f..7d6437dbf5 100644
--- a/src/KOKKOS/improper_harmonic_kokkos.cpp
+++ b/src/KOKKOS/improper_harmonic_kokkos.cpp
@@ -15,23 +15,17 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cmath>
-#include <cstdlib>
 #include "improper_harmonic_kokkos.h"
+#include <cmath>
 #include "atom_kokkos.h"
 #include "comm.h"
 #include "neighbor_kokkos.h"
-#include "domain.h"
 #include "force.h"
-#include "update.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define TOLERANCE 0.05
 #define SMALL     0.001
diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp
index 18a4a3168f..18dff991b2 100644
--- a/src/KOKKOS/kokkos.cpp
+++ b/src/KOKKOS/kokkos.cpp
@@ -11,6 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "kokkos.h"
 #include <mpi.h>
 #include <cstdio>
 #include <cstring>
@@ -18,7 +19,6 @@
 #include <cctype>
 #include <csignal>
 #include <unistd.h>
-#include "kokkos.h"
 #include "lammps.h"
 #include "force.h"
 #include "neighbor_kokkos.h"
@@ -113,23 +113,37 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
       }
       iarg += 2;
 
+      int set_flag = 0;
       char *str;
       if ((str = getenv("SLURM_LOCALID"))) {
         int local_rank = atoi(str);
         device = local_rank % ngpus;
         if (device >= skip_gpu) device++;
+        set_flag = 1;
+      }
+      if ((str = getenv("MPT_LRANK"))) {
+        int local_rank = atoi(str);
+        device = local_rank % ngpus;
+        if (device >= skip_gpu) device++;
+        set_flag = 1;
       }
       if ((str = getenv("MV2_COMM_WORLD_LOCAL_RANK"))) {
         int local_rank = atoi(str);
         device = local_rank % ngpus;
         if (device >= skip_gpu) device++;
+        set_flag = 1;
       }
       if ((str = getenv("OMPI_COMM_WORLD_LOCAL_RANK"))) {
         int local_rank = atoi(str);
         device = local_rank % ngpus;
         if (device >= skip_gpu) device++;
+        set_flag = 1;
       }
 
+      if (ngpus > 1 && !set_flag)
+        error->all(FLERR,"Could not determine local MPI rank for multiple "
+                           "GPUs with Kokkos CUDA because MPI library not recognized");
+
     } else if (strcmp(arg[iarg],"t") == 0 ||
                strcmp(arg[iarg],"threads") == 0) {
       nthreads = atoi(arg[iarg+1]);
@@ -208,6 +222,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   MPI_Comm_size(world,&nmpi);
   if (nmpi > 0) {
 
+#if defined(MPI_VERSION) && (MPI_VERSION > 2)
     // Check for IBM Spectrum MPI
 
     int len;
@@ -226,6 +241,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
         if (me == 0)
           error->warning(FLERR,"The Spectrum MPI '-gpu' flag is not set. Disabling CUDA-aware MPI");
     }
+#endif
 
     if (cuda_aware_flag == 1 && have_cuda_aware == 0) {
       if (me == 0)
@@ -234,10 +250,10 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
       cuda_aware_flag = 0;
     } else if (have_cuda_aware == -1) { // maybe we are dealing with MPICH, MVAPICH2 or some derivative?
     // MVAPICH2
-#if (defined MPICH) && (defined MVAPICH2_VERSION)
+#if defined(MPICH) && defined(MVAPICH2_VERSION)
       char* str;
       cuda_aware_flag = 0;
-      if (str = getenv("MV2_ENABLE_CUDA")
+      if ((str = getenv("MV2_ENABLE_CUDA")))
         if ((strcmp(str,"1") == 0))
           cuda_aware_flag = 1;
 
@@ -245,7 +261,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
         if (me == 0)
           error->warning(FLERR,"MVAPICH2 'MV2_ENABLE_CUDA' environment variable is not set. Disabling CUDA-aware MPI");
     // pure MPICH or some unsupported MPICH derivative
-#elif (defined MPICH) && !(defined MVAPICH2_VERSION)
+#elif defined(MPICH) && !defined(MVAPICH2_VERSION)
       if (me == 0)
         error->warning(FLERR,"Detected MPICH. Disabling CUDA-aware MPI");
       cuda_aware_flag = 0;
diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h
index b9f1e66c68..7b605bee1e 100644
--- a/src/KOKKOS/kokkos.h
+++ b/src/KOKKOS/kokkos.h
@@ -74,6 +74,11 @@ E: Invalid Kokkos command-line args
 
 Self-explanatory.  See Section 2.7 of the manual for details.
 
+E: Could not determine local MPI rank for multiple GPUs with Kokkos CUDA
+because MPI library not recognized
+
+The local MPI rank was not found in one of four supported environment variables.
+
 E: GPUs are requested but Kokkos has not been compiled for CUDA
 
 Recompile Kokkos with CUDA support to use GPUs.
diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h
index 2a19413e0a..3ead8417b9 100644
--- a/src/KOKKOS/kokkos_type.h
+++ b/src/KOKKOS/kokkos_type.h
@@ -14,7 +14,7 @@
 #ifndef LMP_LMPTYPE_KOKKOS_H
 #define LMP_LMPTYPE_KOKKOS_H
 
-#include "lmptype.h"
+#include "pointers.h"
 
 #include <Kokkos_Core.hpp>
 #include <Kokkos_DualView.hpp>
diff --git a/src/KOKKOS/math_special_kokkos.cpp b/src/KOKKOS/math_special_kokkos.cpp
index 127168ef8b..f5fc725347 100644
--- a/src/KOKKOS/math_special_kokkos.cpp
+++ b/src/KOKKOS/math_special_kokkos.cpp
@@ -1,7 +1,7 @@
 
+#include "math_special_kokkos.h"
 #include <cmath>
 #include <cstdint>
-#include "math_special_kokkos.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/KOKKOS/min_cg_kokkos.cpp b/src/KOKKOS/min_cg_kokkos.cpp
new file mode 100644
index 0000000000..47a4513bc0
--- /dev/null
+++ b/src/KOKKOS/min_cg_kokkos.cpp
@@ -0,0 +1,178 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "min_cg_kokkos.h"
+#include <mpi.h>
+#include <cmath>
+#include "update.h"
+#include "output.h"
+#include "timer.h"
+#include "atom_kokkos.h"
+#include "atom_masks.h"
+#include "fix_minimize_kokkos.h"
+
+using namespace LAMMPS_NS;
+
+// EPS_ENERGY = minimum normalization for energy tolerance
+
+#define EPS_ENERGY 1.0e-8
+
+/* ---------------------------------------------------------------------- */
+
+MinCGKokkos::MinCGKokkos(LAMMPS *lmp) : MinLineSearchKokkos(lmp)
+{
+  atomKK = (AtomKokkos *) atom;
+  kokkosable = 1;
+}
+
+/* ----------------------------------------------------------------------
+   minimization via conjugate gradient iterations
+------------------------------------------------------------------------- */
+
+int MinCGKokkos::iterate(int maxiter)
+{
+  int fail,ntimestep;
+  double beta,gg,dot[2],dotall[2];
+
+  fix_minimize_kk->k_vectors.sync<LMPDeviceType>();
+  fix_minimize_kk->k_vectors.modify<LMPDeviceType>();
+
+  // nlimit = max # of CG iterations before restarting
+  // set to ndoftotal unless too big
+
+  int nlimit = static_cast<int> (MIN(MAXSMALLINT,ndoftotal));
+
+  // initialize working vectors
+
+  {
+    // local variables for lambda capture
+
+    auto l_h = h;
+    auto l_g = g;
+    auto l_fvec = fvec;
+
+    Kokkos::parallel_for(nvec, LAMMPS_LAMBDA(const int& i) {
+      l_h[i] = l_fvec[i];
+      l_g[i] = l_fvec[i];
+    });
+  }
+
+  gg = fnorm_sqr();
+
+  for (int iter = 0; iter < maxiter; iter++) {
+
+    if (timer->check_timeout(niter))
+      return TIMEOUT;
+
+    ntimestep = ++update->ntimestep;
+    niter++;
+
+    // line minimization along direction h from current atom->x
+
+    eprevious = ecurrent;
+    fail = (this->*linemin)(ecurrent,alpha_final);
+    if (fail) return fail;
+
+    // function evaluation criterion
+
+    if (neval >= update->max_eval) return MAXEVAL;
+
+    // energy tolerance criterion
+
+    if (fabs(ecurrent-eprevious) <
+        update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
+      return ETOL;
+
+    // force tolerance criterion
+
+    s_double2 sdot;
+    {
+      // local variables for lambda capture
+
+      auto l_g = g;
+      auto l_fvec = fvec;
+
+      Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(const int& i, s_double2& sdot) {
+        sdot.d0 += l_fvec[i]*l_fvec[i];
+        sdot.d1 += l_fvec[i]*l_g[i];
+      },sdot);
+    }
+    dot[0] = sdot.d0;
+    dot[1] = sdot.d1;
+    MPI_Allreduce(dot,dotall,2,MPI_DOUBLE,MPI_SUM,world);
+
+    if (dotall[0] < update->ftol*update->ftol) return FTOL;
+
+    // update new search direction h from new f = -Grad(x) and old g
+    // this is Polak-Ribieri formulation
+    // beta = dotall[0]/gg would be Fletcher-Reeves
+    // reinitialize CG every ndof iterations by setting beta = 0.0
+
+    beta = MAX(0.0,(dotall[0] - dotall[1])/gg);
+    if ((niter+1) % nlimit == 0) beta = 0.0;
+    gg = dotall[0];
+
+    {
+      // local variables for lambda capture
+
+      auto l_h = h;
+      auto l_g = g;
+      auto l_fvec = fvec;
+
+      Kokkos::parallel_for(nvec, LAMMPS_LAMBDA(const int& i) {
+        l_g[i] = l_fvec[i];
+        l_h[i] = l_g[i] + beta*l_h[i];
+      });
+    }
+
+    // reinitialize CG if new search direction h is not downhill
+
+    double dot_0 = 0.0;
+
+    {
+      // local variables for lambda capture
+
+      auto l_h = h;
+      auto l_g = g;
+
+      Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(const int& i, double& dot_0) {
+        dot_0 += l_g[i]*l_h[i];
+      },dot_0);
+    }
+    dot[0] = dot_0;
+    MPI_Allreduce(dot,dotall,1,MPI_DOUBLE,MPI_SUM,world);
+
+    if (dotall[0] <= 0.0) {
+      // local variables for lambda capture
+
+      auto l_h = h;
+      auto l_g = g;
+
+      Kokkos::parallel_for(nvec, LAMMPS_LAMBDA(const int& i) {
+         l_h[i] = l_g[i];
+      });
+    }
+
+    // output for thermo, dump, restart files
+
+    if (output->next == ntimestep) {
+      atomKK->sync(Host,ALL_MASK);
+
+      timer->stamp();
+      output->write(ntimestep);
+      timer->stamp(Timer::OUTPUT);
+    }
+  }
+
+  return MAXITER;
+}
diff --git a/src/KOKKOS/min_cg_kokkos.h b/src/KOKKOS/min_cg_kokkos.h
new file mode 100644
index 0000000000..745bf702c7
--- /dev/null
+++ b/src/KOKKOS/min_cg_kokkos.h
@@ -0,0 +1,38 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef MINIMIZE_CLASS
+
+MinimizeStyle(cg/kk,MinCGKokkos)
+MinimizeStyle(cg/kk/device,MinCGKokkos)
+MinimizeStyle(cg/kk/host,MinCGKokkos)
+
+#else
+
+#ifndef LMP_MIN_CG_KOKKOS_H
+#define LMP_MIN_CG_KOKKOS_H
+
+#include "min_linesearch_kokkos.h"
+
+namespace LAMMPS_NS {
+
+class MinCGKokkos : public MinLineSearchKokkos {
+ public:
+  MinCGKokkos(class LAMMPS *);
+  int iterate(int);
+};
+
+}
+
+#endif
+#endif
diff --git a/src/KOKKOS/min_kokkos.cpp b/src/KOKKOS/min_kokkos.cpp
new file mode 100644
index 0000000000..79ddbbab84
--- /dev/null
+++ b/src/KOKKOS/min_kokkos.cpp
@@ -0,0 +1,631 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Stan Moore (SNL)
+------------------------------------------------------------------------- */
+
+#include "min_kokkos.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include "atom_kokkos.h"
+#include "atom_vec.h"
+#include "domain.h"
+#include "comm.h"
+#include "update.h"
+#include "modify.h"
+#include "fix_minimize_kokkos.h"
+#include "compute.h"
+#include "neighbor.h"
+#include "force.h"
+#include "pair.h"
+#include "bond.h"
+#include "angle.h"
+#include "dihedral.h"
+#include "improper.h"
+#include "kspace.h"
+#include "output.h"
+#include "thermo.h"
+#include "timer.h"
+#include "memory.h"
+#include "error.h"
+#include "kokkos.h"
+#include "atom_masks.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+MinKokkos::MinKokkos(LAMMPS *lmp) : Min(lmp)
+{
+  atomKK = (AtomKokkos *) atom;
+  fix_minimize_kk = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+MinKokkos::~MinKokkos()
+{
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MinKokkos::init()
+{
+  Min::init();
+
+  fix_minimize_kk = (FixMinimizeKokkos*) fix_minimize;
+}
+
+/* ----------------------------------------------------------------------
+   setup before run
+------------------------------------------------------------------------- */
+
+void MinKokkos::setup(int flag)
+{
+  if (comm->me == 0 && screen) {
+    fprintf(screen,"Setting up %s style minimization ...\n",
+            update->minimize_style);
+    if (flag) {
+      fprintf(screen,"  Unit style    : %s\n", update->unit_style);
+      fprintf(screen,"  Current step  : " BIGINT_FORMAT "\n",
+              update->ntimestep);
+      timer->print_timeout(screen);
+    }
+  }
+  update->setupflag = 1;
+
+  // setup extra global dof due to fixes
+  // cannot be done in init() b/c update init() is before modify init()
+
+  nextra_global = modify->min_dof();
+  if (nextra_global) {
+    fextra = new double[nextra_global];
+    if (comm->me == 0 && screen)
+      fprintf(screen,"WARNING: Energy due to %d extra global DOFs will"
+              " be included in minimizer energies\n",nextra_global);
+  }
+
+  // compute for potential energy
+
+  int id = modify->find_compute("thermo_pe");
+  if (id < 0) error->all(FLERR,"Minimization could not find thermo_pe compute");
+  pe_compute = modify->compute[id];
+
+  // style-specific setup does two tasks
+  // setup extra global dof vectors
+  // setup extra per-atom dof vectors due to requests from Pair classes
+  // cannot be done in init() b/c update init() is before modify/pair init()
+
+  setup_style();
+
+  // ndoftotal = total dof for entire minimization problem
+  // dof for atoms, extra per-atom, extra global
+
+  bigint ndofme = 3 * static_cast<bigint>(atom->nlocal);
+  for (int m = 0; m < nextra_atom; m++)
+    ndofme += extra_peratom[m]*atom->nlocal;
+  MPI_Allreduce(&ndofme,&ndoftotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
+  ndoftotal += nextra_global;
+
+  // setup domain, communication and neighboring
+  // acquire ghosts
+  // build neighbor lists
+
+  atom->setup();
+  modify->setup_pre_exchange();
+  if (triclinic) domain->x2lamda(atom->nlocal);
+  domain->pbc();
+  domain->reset_box();
+  comm->setup();
+  if (neighbor->style) neighbor->setup_bins();
+  comm->exchange();
+  if (atom->sortfreq > 0) atom->sort();
+  comm->borders();
+  if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
+  domain->image_check();
+  domain->box_too_small_check();
+  modify->setup_pre_neighbor();
+  neighbor->build(1);
+  modify->setup_post_neighbor();
+  neighbor->ncalls = 0;
+
+  // remove these restriction eventually
+
+  if (searchflag == 0) {
+    if (nextra_global)
+      error->all(FLERR,
+                 "Cannot use a damped dynamics min style with fix box/relax");
+    if (nextra_atom)
+      error->all(FLERR,
+                 "Cannot use a damped dynamics min style with per-atom DOF");
+  }
+
+  if (strcmp(update->minimize_style,"hftn") == 0) {
+    if (nextra_global)
+      error->all(FLERR, "Cannot use hftn min style with fix box/relax");
+    if (nextra_atom)
+      error->all(FLERR, "Cannot use hftn min style with per-atom DOF");
+  }
+
+  // atoms may have migrated in comm->exchange()
+
+  reset_vectors();
+
+  // compute all forces
+
+  force->setup();
+  ev_set(update->ntimestep);
+  force_clear();
+  modify->setup_pre_force(vflag);
+
+  if (pair_compute_flag) {
+    atomKK->sync(force->pair->execution_space,force->pair->datamask_read);
+    force->pair->compute(eflag,vflag);
+    atomKK->modified(force->pair->execution_space,force->pair->datamask_modify);
+    timer->stamp(Timer::PAIR);
+  }
+  else if (force->pair) force->pair->compute_dummy(eflag,vflag);
+
+  if (atomKK->molecular) {
+    if (force->bond) {
+      atomKK->sync(force->bond->execution_space,force->bond->datamask_read);
+      force->bond->compute(eflag,vflag);
+      atomKK->modified(force->bond->execution_space,force->bond->datamask_modify);
+    }
+    if (force->angle) {
+      atomKK->sync(force->angle->execution_space,force->angle->datamask_read);
+      force->angle->compute(eflag,vflag);
+      atomKK->modified(force->angle->execution_space,force->angle->datamask_modify);
+    }
+    if (force->dihedral) {
+      atomKK->sync(force->dihedral->execution_space,force->dihedral->datamask_read);
+      force->dihedral->compute(eflag,vflag);
+      atomKK->modified(force->dihedral->execution_space,force->dihedral->datamask_modify);
+    }
+    if (force->improper) {
+      atomKK->sync(force->improper->execution_space,force->improper->datamask_read);
+      force->improper->compute(eflag,vflag);
+      atomKK->modified(force->improper->execution_space,force->improper->datamask_modify);
+    }
+    timer->stamp(Timer::BOND);
+  }
+
+  if(force->kspace) {
+    force->kspace->setup();
+    if (kspace_compute_flag) {
+      atomKK->sync(force->kspace->execution_space,force->kspace->datamask_read);
+      force->kspace->compute(eflag,vflag);
+      atomKK->modified(force->kspace->execution_space,force->kspace->datamask_modify);
+      timer->stamp(Timer::KSPACE);
+    } else force->kspace->compute_dummy(eflag,vflag);
+  }
+
+  modify->setup_pre_reverse(eflag,vflag);
+  if (force->newton) comm->reverse_comm();
+
+  // update per-atom minimization variables stored by pair styles
+
+  if (nextra_atom)
+    for (int m = 0; m < nextra_atom; m++)
+      requestor[m]->min_xf_get(m);
+
+  lmp->kokkos->auto_sync = 0;
+  modify->setup(vflag);
+  output->setup(flag);
+  lmp->kokkos->auto_sync = 1;
+  update->setupflag = 0;
+
+  // stats for initial thermo output
+
+  ecurrent = pe_compute->compute_scalar();
+  if (nextra_global) ecurrent += modify->min_energy(fextra);
+  if (output->thermo->normflag) ecurrent /= atom->natoms;
+
+  einitial = ecurrent;
+  fnorm2_init = sqrt(fnorm_sqr());
+  fnorminf_init = fnorm_inf();
+}
+
+/* ----------------------------------------------------------------------
+   setup without output or one-time post-init setup
+   flag = 0 = just force calculation
+   flag = 1 = reneighbor and force calculation
+------------------------------------------------------------------------- */
+
+void MinKokkos::setup_minimal(int flag)
+{
+  update->setupflag = 1;
+
+  // setup domain, communication and neighboring
+  // acquire ghosts
+  // build neighbor lists
+
+  if (flag) {
+    modify->setup_pre_exchange();
+    if (triclinic) domain->x2lamda(atom->nlocal);
+    domain->pbc();
+    domain->reset_box();
+    comm->setup();
+    if (neighbor->style) neighbor->setup_bins();
+    comm->exchange();
+    comm->borders();
+    if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
+    domain->image_check();
+    domain->box_too_small_check();
+    modify->setup_pre_neighbor();
+    neighbor->build(1);
+    modify->setup_post_neighbor();
+    neighbor->ncalls = 0;
+  }
+
+  // atoms may have migrated in comm->exchange()
+
+  reset_vectors();
+
+  // compute all forces
+
+  ev_set(update->ntimestep);
+  force_clear();
+  modify->setup_pre_force(vflag);
+
+  if (pair_compute_flag) {
+    atomKK->sync(force->pair->execution_space,force->pair->datamask_read);
+    force->pair->compute(eflag,vflag);
+    atomKK->modified(force->pair->execution_space,force->pair->datamask_modify);
+    timer->stamp(Timer::PAIR);
+  }
+  else if (force->pair) force->pair->compute_dummy(eflag,vflag);
+
+  if (atomKK->molecular) {
+    if (force->bond) {
+      atomKK->sync(force->bond->execution_space,force->bond->datamask_read);
+      force->bond->compute(eflag,vflag);
+      atomKK->modified(force->bond->execution_space,force->bond->datamask_modify);
+    }
+    if (force->angle) {
+      atomKK->sync(force->angle->execution_space,force->angle->datamask_read);
+      force->angle->compute(eflag,vflag);
+      atomKK->modified(force->angle->execution_space,force->angle->datamask_modify);
+    }
+    if (force->dihedral) {
+      atomKK->sync(force->dihedral->execution_space,force->dihedral->datamask_read);
+      force->dihedral->compute(eflag,vflag);
+      atomKK->modified(force->dihedral->execution_space,force->dihedral->datamask_modify);
+    }
+    if (force->improper) {
+      atomKK->sync(force->improper->execution_space,force->improper->datamask_read);
+      force->improper->compute(eflag,vflag);
+      atomKK->modified(force->improper->execution_space,force->improper->datamask_modify);
+    }
+    timer->stamp(Timer::BOND);
+  }
+
+  if(force->kspace) {
+    force->kspace->setup();
+    if (kspace_compute_flag) {
+      atomKK->sync(force->kspace->execution_space,force->kspace->datamask_read);
+      force->kspace->compute(eflag,vflag);
+      atomKK->modified(force->kspace->execution_space,force->kspace->datamask_modify);
+      timer->stamp(Timer::KSPACE);
+    } else force->kspace->compute_dummy(eflag,vflag);
+  }
+
+  modify->setup_pre_reverse(eflag,vflag);
+  if (force->newton) comm->reverse_comm();
+
+  // update per-atom minimization variables stored by pair styles
+
+  if (nextra_atom)
+    for (int m = 0; m < nextra_atom; m++)
+      requestor[m]->min_xf_get(m);
+
+  lmp->kokkos->auto_sync = 0;
+  modify->setup(vflag);
+  lmp->kokkos->auto_sync = 1;
+  update->setupflag = 0;
+
+  // stats for Finish to print
+
+  ecurrent = pe_compute->compute_scalar();
+  if (nextra_global) ecurrent += modify->min_energy(fextra);
+  if (output->thermo->normflag) ecurrent /= atom->natoms;
+
+  einitial = ecurrent;
+  fnorm2_init = sqrt(fnorm_sqr());
+  fnorminf_init = fnorm_inf();
+}
+
+/* ----------------------------------------------------------------------
+   perform minimization, calling iterate() for N steps
+------------------------------------------------------------------------- */
+
+void MinKokkos::run(int n)
+{
+  if (nextra_global)
+    error->all(FLERR,"Cannot yet use extra global DOFs (e.g. fix box/relax) "
+     "with Kokkos minimize");
+
+  if (nextra_global || nextra_atom)
+    error->all(FLERR,"Cannot yet use extra atom DOFs (e.g. USER-AWPMD and USER-EFF packages) "
+     "with Kokkos minimize");
+
+  // minimizer iterations
+
+  lmp->kokkos->auto_sync = 0;
+  atomKK->sync(Device,ALL_MASK);
+
+  stop_condition = iterate(n);
+  stopstr = stopstrings(stop_condition);
+
+  // if early exit from iterate loop:
+  // set update->nsteps to niter for Finish stats to print
+  // set output->next values to this timestep
+  // call energy_force() to insure vflag is set when forces computed
+  // output->write does final output for thermo, dump, restart files
+  // add ntimestep to all computes that store invocation times
+  //   since are hardwiring call to thermo/dumps and computes may not be ready
+
+  if (stop_condition != MAXITER) {
+    update->nsteps = niter;
+
+    if (update->restrict_output == 0) {
+      for (int idump = 0; idump < output->ndump; idump++)
+        output->next_dump[idump] = update->ntimestep;
+      output->next_dump_any = update->ntimestep;
+      if (output->restart_flag) {
+        output->next_restart = update->ntimestep;
+        if (output->restart_every_single)
+          output->next_restart_single = update->ntimestep;
+        if (output->restart_every_double)
+          output->next_restart_double = update->ntimestep;
+      }
+    }
+    output->next_thermo = update->ntimestep;
+
+    modify->addstep_compute_all(update->ntimestep);
+    ecurrent = energy_force(0);
+
+    atomKK->sync(Host,ALL_MASK);
+    output->write(update->ntimestep);
+  }
+
+  atomKK->sync(Host,ALL_MASK);
+  lmp->kokkos->auto_sync = 1;
+}
+
+/* ----------------------------------------------------------------------
+   evaluate potential energy and forces
+   may migrate atoms due to reneighboring
+   return new energy, which should include nextra_global dof
+   return negative gradient stored in atom->f
+   return negative gradient for nextra_global dof in fextra
+------------------------------------------------------------------------- */
+
+double MinKokkos::energy_force(int resetflag)
+{
+  // check for reneighboring
+  // always communicate since minimizer moved atoms
+
+  int nflag = neighbor->decide();
+
+  if (nflag == 0) {
+    timer->stamp();
+    comm->forward_comm();
+    timer->stamp(Timer::COMM);
+  } else {
+    if (modify->n_min_pre_exchange) {
+      timer->stamp();
+      modify->min_pre_exchange();
+      timer->stamp(Timer::MODIFY);
+    }
+    if (triclinic) domain->x2lamda(atom->nlocal);
+    domain->pbc();
+    if (domain->box_change) {
+      domain->reset_box();
+      comm->setup();
+      if (neighbor->style) neighbor->setup_bins();
+    }
+    timer->stamp();
+    comm->exchange();
+    if (atom->sortfreq > 0 &&
+        update->ntimestep >= atom->nextsort) atom->sort();
+    comm->borders();
+    if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
+    timer->stamp(Timer::COMM);
+    if (modify->n_min_pre_neighbor) {
+      modify->min_pre_neighbor();
+      timer->stamp(Timer::MODIFY);
+    }
+    neighbor->build(1);
+    timer->stamp(Timer::NEIGH);
+    if (modify->n_min_post_neighbor) {
+      modify->min_post_neighbor();
+      timer->stamp(Timer::MODIFY);
+    }
+  }
+
+  ev_set(update->ntimestep);
+  force_clear();
+
+  timer->stamp();
+
+  if (modify->n_min_pre_force) {
+    modify->min_pre_force(vflag);
+    timer->stamp(Timer::MODIFY);
+  }
+
+  if (pair_compute_flag) {
+    atomKK->sync(force->pair->execution_space,force->pair->datamask_read);
+    force->pair->compute(eflag,vflag);
+    atomKK->modified(force->pair->execution_space,force->pair->datamask_modify);
+    timer->stamp(Timer::PAIR);
+  }
+
+  if (atom->molecular) {
+    if (force->bond) {
+      atomKK->sync(force->bond->execution_space,force->bond->datamask_read);
+      force->bond->compute(eflag,vflag);
+      atomKK->modified(force->bond->execution_space,force->bond->datamask_modify);
+    }
+    if (force->angle) {
+      atomKK->sync(force->angle->execution_space,force->angle->datamask_read);
+      force->angle->compute(eflag,vflag);
+      atomKK->modified(force->angle->execution_space,force->angle->datamask_modify);
+    }
+    if (force->dihedral) {
+      atomKK->sync(force->dihedral->execution_space,force->dihedral->datamask_read);
+      force->dihedral->compute(eflag,vflag);
+      atomKK->modified(force->dihedral->execution_space,force->dihedral->datamask_modify);
+    }
+    if (force->improper) {
+      atomKK->sync(force->improper->execution_space,force->improper->datamask_read);
+      force->improper->compute(eflag,vflag);
+      atomKK->modified(force->improper->execution_space,force->improper->datamask_modify);
+    }
+    timer->stamp(Timer::BOND);
+  }
+
+  if (kspace_compute_flag) {
+    atomKK->sync(force->kspace->execution_space,force->kspace->datamask_read);
+    force->kspace->compute(eflag,vflag);
+    atomKK->modified(force->kspace->execution_space,force->kspace->datamask_modify);
+    timer->stamp(Timer::KSPACE);
+  }
+
+  if (modify->n_min_pre_reverse) {
+    modify->min_pre_reverse(eflag,vflag);
+    timer->stamp(Timer::MODIFY);
+  }
+
+  if (force->newton) {
+    comm->reverse_comm();
+    timer->stamp(Timer::COMM);
+  }
+
+  // fixes that affect minimization
+
+  if (modify->n_min_post_force) {
+     timer->stamp();
+     modify->min_post_force(vflag);
+     timer->stamp(Timer::MODIFY);
+  }
+
+  // compute potential energy of system
+  // normalize if thermo PE does
+
+  atomKK->sync(pe_compute->execution_space,pe_compute->datamask_read);
+  double energy = pe_compute->compute_scalar();
+  atomKK->modified(pe_compute->execution_space,pe_compute->datamask_modify);
+  if (nextra_global) energy += modify->min_energy(fextra);
+  if (output->thermo->normflag) energy /= atom->natoms;
+
+  // if reneighbored, atoms migrated
+  // if resetflag = 1, update x0 of atoms crossing PBC
+  // reset vectors used by lo-level minimizer
+
+  if (nflag) {
+    if (resetflag) fix_minimize_kk->reset_coords();
+    reset_vectors();
+  }
+  return energy;
+}
+
+/* ----------------------------------------------------------------------
+   clear force on own & ghost atoms
+   clear other arrays as needed
+------------------------------------------------------------------------- */
+
+void MinKokkos::force_clear()
+{
+  if (external_force_clear) return;
+
+  // clear global force array
+  // if either newton flag is set, also include ghosts
+
+  atomKK->k_f.clear_sync_state(); // ignore host forces/torques since device views
+  atomKK->k_torque.clear_sync_state(); // will be cleared below
+
+  int nzero = atom->nlocal;
+  if (force->newton) nzero += atom->nghost;
+
+  if (nzero) {
+    // local variables for lambda capture
+
+    auto l_f = atomKK->k_f.d_view;
+    auto l_torque = atomKK->k_torque.d_view;
+    auto l_torqueflag = torqueflag;
+
+    Kokkos::parallel_for(nzero, LAMMPS_LAMBDA(int i) {
+      l_f(i,0) = 0.0;
+      l_f(i,1) = 0.0;
+      l_f(i,2) = 0.0;
+      if (l_torqueflag) {
+        l_torque(i,0) = 0.0;
+        l_torque(i,1) = 0.0;
+        l_torque(i,2) = 0.0;
+      }
+    });
+  }
+  atomKK->modified(Device,F_MASK);
+}
+
+/* ----------------------------------------------------------------------
+   compute and return ||force||_2^2
+------------------------------------------------------------------------- */
+
+double MinKokkos::fnorm_sqr()
+{
+
+  double local_norm2_sqr = 0.0;
+  {
+    // local variables for lambda capture
+
+    auto l_fvec = fvec;
+
+    Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(int i, double& local_norm2_sqr) {
+      local_norm2_sqr += l_fvec[i]*l_fvec[i];
+    },local_norm2_sqr);
+  }
+
+  double norm2_sqr = 0.0;
+  MPI_Allreduce(&local_norm2_sqr,&norm2_sqr,1,MPI_DOUBLE,MPI_SUM,world);
+
+  return norm2_sqr;
+}
+
+/* ----------------------------------------------------------------------
+   compute and return ||force||_inf
+------------------------------------------------------------------------- */
+
+double MinKokkos::fnorm_inf()
+{
+
+  double local_norm_inf = 0.0;
+  {
+    // local variables for lambda capture
+
+    auto l_fvec = fvec;
+
+    Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(int i, double& local_norm_inf) {
+      local_norm_inf = MAX(fabs(l_fvec[i]),local_norm_inf);
+    },Kokkos::Max<double>(local_norm_inf));
+  }
+
+  double norm_inf = 0.0;
+  MPI_Allreduce(&local_norm_inf,&norm_inf,1,MPI_DOUBLE,MPI_MAX,world);
+
+  return norm_inf;
+}
diff --git a/src/KOKKOS/min_kokkos.h b/src/KOKKOS/min_kokkos.h
new file mode 100644
index 0000000000..49cd1d1849
--- /dev/null
+++ b/src/KOKKOS/min_kokkos.h
@@ -0,0 +1,58 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_MIN_KOKKOS_H
+#define LMP_MIN_KOKKOS_H
+
+#include "min.h"
+#include "kokkos_type.h"
+
+namespace LAMMPS_NS {
+
+class MinKokkos : public Min {
+ public:
+  MinKokkos(class LAMMPS *);
+  virtual ~MinKokkos();
+  void init();
+  void setup(int flag=1);
+  void setup_minimal(int);
+  void run(int);
+  double fnorm_sqr();
+  double fnorm_inf();
+
+  virtual void init_style() {}
+  virtual void setup_style() = 0;
+  virtual void reset_vectors() = 0;
+  virtual int iterate(int) = 0;
+
+  // possible return values of iterate() method
+  enum{MAXITER,MAXEVAL,ETOL,FTOL,DOWNHILL,ZEROALPHA,ZEROFORCE,
+       ZEROQUAD,TRSMALL,INTERROR,TIMEOUT};
+
+ //protected: // won't compile with CUDA
+  class FixMinimizeKokkos *fix_minimize_kk;  // fix that stores auxiliary data
+
+  DAT::t_ffloat_1d xvec;            // variables for atomic dof, as 1d vector
+  DAT::t_ffloat_1d fvec;            // force vector for atomic dof, as 1d vector
+
+  double energy_force(int);
+  void force_clear();
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/KOKKOS/min_linesearch_kokkos.cpp b/src/KOKKOS/min_linesearch_kokkos.cpp
new file mode 100644
index 0000000000..cb07c7db86
--- /dev/null
+++ b/src/KOKKOS/min_linesearch_kokkos.cpp
@@ -0,0 +1,401 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Stan Moore (SNL)
+------------------------------------------------------------------------- */
+
+#include "min_linesearch_kokkos.h"
+#include <mpi.h>
+#include <cmath>
+#include "atom_kokkos.h"
+#include "modify.h"
+#include "fix_minimize_kokkos.h"
+#include "pair.h"
+#include "output.h"
+#include "thermo.h"
+#include "error.h"
+#include "atom_masks.h"
+
+using namespace LAMMPS_NS;
+
+// ALPHA_MAX = max alpha allowed to avoid long backtracks
+// ALPHA_REDUCE = reduction ratio, should be in range [0.5,1)
+// BACKTRACK_SLOPE, should be in range (0,0.5]
+// QUADRATIC_TOL = tolerance on alpha0, should be in range [0.1,1)
+// EMACH = machine accuracy limit of energy changes (1.0e-8)
+// EPS_QUAD = tolerance for quadratic projection
+
+#define ALPHA_MAX 1.0
+#define ALPHA_REDUCE 0.5
+#define BACKTRACK_SLOPE 0.4
+#define QUADRATIC_TOL 0.1
+//#define EMACH 1.0e-8
+#define EMACH 1.0e-8
+#define EPS_QUAD 1.0e-28
+
+/* ---------------------------------------------------------------------- */
+
+MinLineSearchKokkos::MinLineSearchKokkos(LAMMPS *lmp) : MinKokkos(lmp)
+{
+  searchflag = 1;
+  atomKK = (AtomKokkos *) atom;
+}
+
+/* ---------------------------------------------------------------------- */
+
+MinLineSearchKokkos::~MinLineSearchKokkos()
+{
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MinLineSearchKokkos::init()
+{
+  MinKokkos::init();
+
+  if (linestyle == 1) linemin = &MinLineSearchKokkos::linemin_quadratic;
+  else error->all(FLERR,"Kokkos minimize only supports the 'min_modify line "
+   "quadratic' option");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MinLineSearchKokkos::setup_style()
+{
+  // memory for x0,g,h for atomic dof
+
+  fix_minimize_kk->add_vector_kokkos();
+  fix_minimize_kk->add_vector_kokkos();
+  fix_minimize_kk->add_vector_kokkos();
+}
+
+/* ----------------------------------------------------------------------
+   set current vector lengths and pointers
+   called after atoms have migrated
+------------------------------------------------------------------------- */
+
+void MinLineSearchKokkos::reset_vectors()
+{
+  // atomic dof
+
+  nvec = 3 * atom->nlocal;
+  atomKK->sync(Device,F_MASK|X_MASK);
+  auto d_x = atomKK->k_x.d_view;
+  auto d_f = atomKK->k_f.d_view;
+
+  if (nvec) xvec = DAT::t_ffloat_1d(d_x.data(),d_x.size());
+  if (nvec) fvec = DAT::t_ffloat_1d(d_f.data(),d_f.size());
+  x0 = fix_minimize_kk->request_vector_kokkos(0);
+  g = fix_minimize_kk->request_vector_kokkos(1);
+  h = fix_minimize_kk->request_vector_kokkos(2);
+
+  auto h_fvec = Kokkos::create_mirror_view(fvec);
+  Kokkos::deep_copy(h_fvec,fvec);
+}
+
+/* ----------------------------------------------------------------------
+   line minimization methods
+   find minimum-energy starting at x along h direction
+   input args:   eoriginal = energy at initial x
+   input extra:  n,x,x0,f,h for atomic, extra global, extra per-atom dof
+   output args:  return 0 if successful move, non-zero alpha
+                 return non-zero if failed
+                 alpha = distance moved along h for x at min eng config
+                 update neval counter of eng/force function evaluations
+                 output extra: if fail, energy_force() of original x
+                 if succeed, energy_force() at x + alpha*h
+                 atom->x = coords at new configuration
+                 atom->f = force at new configuration
+                 ecurrent = energy of new configuration
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+    // linemin: quadratic line search (adapted from Dennis and Schnabel)
+    // The objective function is approximated by a quadratic
+    // function in alpha, for sufficiently small alpha.
+    // This idea is the same as that used in the well-known secant
+    // method. However, since the change in the objective function
+    // (difference of two finite numbers) is not known as accurately
+    // as the gradient (which is close to zero), all the expressions
+    // are written in terms of gradients. In this way, we can converge
+    // the LAMMPS forces much closer to zero.
+    //
+    // We know E,Eprev,fh,fhprev. The Taylor series about alpha_prev
+    // truncated at the quadratic term is:
+    //
+    //     E = Eprev - del_alpha*fhprev + (1/2)del_alpha^2*Hprev
+    //
+    // and
+    //
+    //     fh = fhprev - del_alpha*Hprev
+    //
+    // where del_alpha = alpha-alpha_prev
+    //
+    // We solve these two equations for Hprev and E=Esolve, giving:
+    //
+    //     Esolve = Eprev - del_alpha*(f+fprev)/2
+    //
+    // We define relerr to be:
+    //
+    //      relerr = |(Esolve-E)/Eprev|
+    //             = |1.0 - (0.5*del_alpha*(f+fprev)+E)/Eprev|
+    //
+    // If this is accurate to within a reasonable tolerance, then
+    // we go ahead and use a secant step to fh = 0:
+    //
+    //      alpha0 = alpha - (alpha-alphaprev)*fh/delfh;
+    //
+------------------------------------------------------------------------- */
+
+int MinLineSearchKokkos::linemin_quadratic(double eoriginal, double &alpha)
+{
+  double fdothall,fdothme,hme,hmaxall;
+  double de_ideal,de;
+  double delfh,engprev,relerr,alphaprev,fhprev,ff,fh,alpha0;
+  double dot[2],dotall[2];
+  double alphamax;
+
+  fix_minimize_kk->k_vectors.sync<LMPDeviceType>();
+  fix_minimize_kk->k_vectors.modify<LMPDeviceType>();
+
+  // fdothall = projection of search dir along downhill gradient
+  // if search direction is not downhill, exit with error
+
+  fdothme = 0.0;
+  {
+    // local variables for lambda capture
+
+    auto l_fvec = fvec;
+    auto l_h = h;
+
+    Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(const int& i, double& fdothme) {
+      fdothme += l_fvec[i]*l_h[i];
+    },fdothme);
+  }
+  MPI_Allreduce(&fdothme,&fdothall,1,MPI_DOUBLE,MPI_SUM,world);
+  if (output->thermo->normflag) fdothall /= atom->natoms;
+
+  if (fdothall <= 0.0) return DOWNHILL;
+
+  // set alphamax so no dof is changed by more than max allowed amount
+  // for atom coords, max amount = dmax
+  // for extra per-atom dof, max amount = extra_max[]
+  // for extra global dof, max amount is set by fix
+  // also insure alphamax <= ALPHA_MAX
+  // else will have to backtrack from huge value when forces are tiny
+  // if all search dir components are already 0.0, exit with error
+
+
+  hme = 0.0;
+  {
+    // local variables for lambda capture
+
+    auto l_h = h;
+
+    Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(const int& i, double& hme) {
+      hme = MAX(hme,fabs(l_h[i]));
+    },Kokkos::Max<double>(hme));
+  }
+  MPI_Allreduce(&hme,&hmaxall,1,MPI_DOUBLE,MPI_MAX,world);
+  alphamax = MIN(ALPHA_MAX,dmax/hmaxall);
+
+  if (hmaxall == 0.0) return ZEROFORCE;
+
+  // store box and values of all dof at start of linesearch
+
+  {
+    // local variables for lambda capture
+
+    auto l_xvec = xvec;
+    auto l_x0 = x0;
+
+    fix_minimize_kk->store_box();
+    Kokkos::parallel_for(nvec, LAMMPS_LAMBDA(const int& i) {
+      l_x0[i] = l_xvec[i];
+    });
+  }
+
+  // backtrack with alpha until energy decrease is sufficient
+  // or until get to small energy change, then perform quadratic projection
+
+  alpha = alphamax;
+  fhprev = fdothall;
+  engprev = eoriginal;
+  alphaprev = 0.0;
+
+  // // important diagnostic: test the gradient against energy
+  // double etmp;
+  // double alphatmp = alphamax*1.0e-4;
+  // etmp = alpha_step(alphatmp,1);
+  // printf("alpha = %g dele = %g dele_force = %g err = %g\n",
+  //        alphatmp,etmp-eoriginal,-alphatmp*fdothall,
+  //        etmp-eoriginal+alphatmp*fdothall);
+  // alpha_step(0.0,1);
+
+  while (1) {
+    ecurrent = alpha_step(alpha,1);
+
+    // compute new fh, alpha, delfh
+
+    s_double2 sdot;
+    {
+      // local variables for lambda capture
+
+      auto l_fvec = fvec;
+      auto l_h = h;
+
+      Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(const int& i, s_double2& sdot) {
+        sdot.d0 += l_fvec[i]*l_fvec[i];
+        sdot.d1 += l_fvec[i]*l_h[i];
+      },sdot);
+    }
+    dot[0] = sdot.d0;
+    dot[1] = sdot.d1;
+
+    MPI_Allreduce(dot,dotall,2,MPI_DOUBLE,MPI_SUM,world);
+    ff = dotall[0];
+    fh = dotall[1];
+    if (output->thermo->normflag) {
+      ff /= atom->natoms;
+      fh /= atom->natoms;
+    }
+
+    delfh = fh - fhprev;
+
+    // if fh or delfh is epsilon, reset to starting point, exit with error
+
+    if (fabs(fh) < EPS_QUAD || fabs(delfh) < EPS_QUAD) {
+      ecurrent = alpha_step(0.0,0);
+      return ZEROQUAD;
+    }
+
+    // Check if ready for quadratic projection, equivalent to secant method
+    // alpha0 = projected alpha
+
+    relerr = fabs(1.0-(0.5*(alpha-alphaprev)*(fh+fhprev)+ecurrent)/engprev);
+    alpha0 = alpha - (alpha-alphaprev)*fh/delfh;
+
+    if (relerr <= QUADRATIC_TOL && alpha0 > 0.0 && alpha0 < alphamax) {
+      ecurrent = alpha_step(alpha0,1);
+      if (ecurrent - eoriginal < EMACH) {
+        return 0;
+      }
+    }
+
+    // if backtracking energy change is better than ideal, exit with success
+
+    de_ideal = -BACKTRACK_SLOPE*alpha*fdothall;
+    de = ecurrent - eoriginal;
+
+    if (de <= de_ideal)
+      return 0;
+
+    // save previous state
+
+    fhprev = fh;
+    engprev = ecurrent;
+    alphaprev = alpha;
+
+    // reduce alpha
+
+    alpha *= ALPHA_REDUCE;
+
+    // backtracked all the way to 0.0
+    // reset to starting point, exit with error
+
+    if (alpha <= 0.0 || de_ideal >= -EMACH) {
+      ecurrent = alpha_step(0.0,0);
+      return ZEROALPHA;
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+double MinLineSearchKokkos::alpha_step(double alpha, int resetflag)
+{
+  // reset to starting point
+
+  atomKK->k_x.clear_sync_state(); // ignore if host positions since device
+                                  //  positions will be reset below
+  {
+    // local variables for lambda capture
+
+    auto l_xvec = xvec;
+    auto l_x0 = x0;
+
+    Kokkos::parallel_for(nvec, LAMMPS_LAMBDA(const int& i) {
+      l_xvec[i] = l_x0[i];
+    });
+  }
+
+  // step forward along h
+
+  if (alpha > 0.0) {
+    // local variables for lambda capture
+
+    auto l_xvec = xvec;
+    auto l_h = h;
+
+    Kokkos::parallel_for(nvec, LAMMPS_LAMBDA(const int& i) {
+      l_xvec[i] += alpha*l_h[i];
+    });
+  }
+
+  atomKK->modified(Device,X_MASK);
+
+  // compute and return new energy
+
+  neval++;
+  return energy_force(resetflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+// compute projection of force on: itself and the search direction
+
+double MinLineSearchKokkos::compute_dir_deriv(double &ff)
+{
+  double dot[2],dotall[2];
+  double fh;
+
+  // compute new fh, alpha, delfh
+
+  s_double2 sdot;
+  {
+    // local variables for lambda capture
+
+    auto l_fvec = fvec;
+    auto l_h = h;
+
+    Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(const int& i, s_double2& sdot) {
+      sdot.d0 += l_fvec[i]*l_fvec[i];
+      sdot.d1 += l_fvec[i]*l_h[i];
+    },sdot);
+  }
+  dot[0] = sdot.d0;
+  dot[1] = sdot.d1;
+
+  MPI_Allreduce(dot,dotall,2,MPI_DOUBLE,MPI_SUM,world);
+
+  ff = dotall[0];
+  fh = dotall[1];
+  if (output->thermo->normflag) {
+    ff /= atom->natoms;
+    fh /= atom->natoms;
+  }
+
+  return fh;
+}
diff --git a/src/KOKKOS/min_linesearch_kokkos.h b/src/KOKKOS/min_linesearch_kokkos.h
new file mode 100644
index 0000000000..70df13d1e7
--- /dev/null
+++ b/src/KOKKOS/min_linesearch_kokkos.h
@@ -0,0 +1,69 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_MIN_LSRCH_KOKKOS_H
+#define LMP_MIN_LSRCH_KOKKOS_H
+
+#include "min_kokkos.h"
+
+namespace LAMMPS_NS {
+
+  struct s_double2 {
+    double d0, d1;
+    KOKKOS_INLINE_FUNCTION
+    s_double2() {
+      d0 = d1 = 0.0;
+    }
+    KOKKOS_INLINE_FUNCTION
+    s_double2& operator+=(const s_double2 &rhs){
+      d0 += rhs.d0;
+      d1 += rhs.d1;
+      return *this;
+    }
+
+    KOKKOS_INLINE_FUNCTION
+    void operator+=(const volatile s_double2 &rhs) volatile {
+      d0 += rhs.d0;
+      d1 += rhs.d1;
+    }
+  };
+  //typedef s_double2 double2;
+
+class MinLineSearchKokkos : public MinKokkos {
+ public:
+  MinLineSearchKokkos(class LAMMPS *);
+  ~MinLineSearchKokkos();
+  void init();
+  void setup_style();
+  void reset_vectors();
+
+ //protected: // won't compile with CUDA
+  // vectors needed by linesearch minimizers
+  // allocated and stored by fix_minimize
+  // x,f are stored by parent or Atom class or Pair class
+
+  DAT::t_ffloat_1d x0;   // coords at start of linesearch
+  DAT::t_ffloat_1d g;    // old gradient vector
+  DAT::t_ffloat_1d h;    // search direction vector
+
+  typedef int (MinLineSearchKokkos::*FnPtr)(double, double &);
+  FnPtr linemin;
+  int linemin_quadratic(double, double &);
+
+  double alpha_step(double, int);
+  double compute_dir_deriv(double &);
+};
+
+}
+
+#endif
diff --git a/src/KOKKOS/nbin_ssa_kokkos.cpp b/src/KOKKOS/nbin_ssa_kokkos.cpp
index ecf0e08535..0e46f7fc61 100644
--- a/src/KOKKOS/nbin_ssa_kokkos.cpp
+++ b/src/KOKKOS/nbin_ssa_kokkos.cpp
@@ -19,11 +19,8 @@
 #include "nbin_ssa_kokkos.h"
 #include "neighbor.h"
 #include "atom_kokkos.h"
-#include "group.h"
 #include "domain.h"
-#include "comm.h"
 #include "update.h"
-#include "error.h"
 #include "atom_masks.h"
 
 // #include "memory_kokkos.h"
diff --git a/src/KOKKOS/npair_copy_kokkos.cpp b/src/KOKKOS/npair_copy_kokkos.cpp
index 7dde05745c..0ce0f4d3ff 100644
--- a/src/KOKKOS/npair_copy_kokkos.cpp
+++ b/src/KOKKOS/npair_copy_kokkos.cpp
@@ -12,14 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_copy_kokkos.h"
-#include "neighbor.h"
 #include "neigh_list_kokkos.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
-#include "my_page.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/KOKKOS/npair_skip_kokkos.cpp b/src/KOKKOS/npair_skip_kokkos.cpp
index e614e624c9..bb393c9b95 100644
--- a/src/KOKKOS/npair_skip_kokkos.cpp
+++ b/src/KOKKOS/npair_skip_kokkos.cpp
@@ -12,13 +12,9 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_skip_kokkos.h"
-#include "neighbor.h"
 #include "neigh_list_kokkos.h"
 #include "atom_kokkos.h"
 #include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
-#include "my_page.h"
 #include "error.h"
 #include "atom_masks.h"
 
diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
index 57ac3a9c57..2a72617525 100644
--- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
@@ -15,20 +15,16 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_buck_coul_cut_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "math_const.h"
 #include "memory_kokkos.h"
diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
index 349c4c0601..fdf395684a 100644
--- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
@@ -15,28 +15,22 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_buck_coul_long_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp
index 02c02c986e..375d0dc1ea 100644
--- a/src/KOKKOS/pair_buck_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_kokkos.cpp
@@ -15,28 +15,22 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_buck_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp
index 54ba0b63ce..5a1a6eefac 100644
--- a/src/KOKKOS/pair_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp
@@ -11,28 +11,19 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_cut_kokkos.h"
+#include <cmath>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp
index 8966e30394..8dd7e4f3d2 100644
--- a/src/KOKKOS/pair_coul_debye_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp
@@ -15,28 +15,22 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_debye_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp
index 748fed71a7..836b12ba39 100644
--- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp
@@ -15,22 +15,15 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_dsf_kokkos.h"
+#include <cmath>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list_kokkos.h"
 #include "neigh_request.h"
 #include "memory_kokkos.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
 #include "math_const.h"
 #include "error.h"
 #include "atom_masks.h"
diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp
index a21cb050ff..84b89c6373 100644
--- a/src/KOKKOS/pair_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_long_kokkos.cpp
@@ -15,28 +15,22 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_long_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp
index 20391d9530..3ca8f16a79 100644
--- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp
@@ -15,21 +15,14 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_wolf_kokkos.h"
+#include <cmath>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list_kokkos.h"
 #include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
 #include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp
index a44ef1790e..21fd32a2c8 100644
--- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp
+++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp
@@ -15,22 +15,16 @@
    Contributing author: Stan Moore (Sandia)
 ------------------------------------------------------------------------- */
 
+#include "pair_dpd_fdt_energy_kokkos.h"
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "atom_kokkos.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "update.h"
-#include "fix.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "memory_kokkos.h"
-#include "modify.h"
-#include "pair_dpd_fdt_energy_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 #include "kokkos.h"
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index b5442c0d29..48bf63386a 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -15,13 +15,11 @@
    Contributing authors: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_eam_alloy_kokkos.h"
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "kokkos.h"
 #include "pair_kokkos.h"
-#include "pair_eam_alloy_kokkos.h"
 #include "atom_kokkos.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h
index 6593ccae73..e1dd9ab47d 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.h
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.h
@@ -23,7 +23,6 @@ PairStyle(eam/alloy/kk/host,PairEAMAlloyKokkos<LMPHostType>)
 #ifndef LMP_PAIR_EAM_ALLOY_KOKKOS_H
 #define LMP_PAIR_EAM_ALLOY_KOKKOS_H
 
-#include <cstdio>
 #include "kokkos_base.h"
 #include "pair_kokkos.h"
 #include "pair_eam.h"
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp
index 16701febd6..6536dd745a 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
@@ -15,13 +15,11 @@
    Contributing authors: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_eam_fs_kokkos.h"
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "kokkos.h"
 #include "pair_kokkos.h"
-#include "pair_eam_fs_kokkos.h"
 #include "atom_kokkos.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h
index f75605ff6d..e93977869e 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.h
+++ b/src/KOKKOS/pair_eam_fs_kokkos.h
@@ -23,7 +23,6 @@ PairStyle(eam/fs/kk/host,PairEAMFSKokkos<LMPHostType>)
 #ifndef LMP_PAIR_EAM_FS_KOKKOS_H
 #define LMP_PAIR_EAM_FS_KOKKOS_H
 
-#include <cstdio>
 #include "kokkos_base.h"
 #include "pair_kokkos.h"
 #include "pair_eam.h"
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index d423f2c927..f6eef5b53c 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -15,13 +15,10 @@
    Contributing authors: Stan Moore (SNL), Christian Trott (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_eam_kokkos.h"
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "kokkos.h"
 #include "pair_kokkos.h"
-#include "pair_eam_kokkos.h"
 #include "atom_kokkos.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h
index 4040eba858..3bf89c549a 100644
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
@@ -23,7 +23,6 @@ PairStyle(eam/kk/host,PairEAMKokkos<LMPHostType>)
 #ifndef LMP_PAIR_EAM_KOKKOS_H
 #define LMP_PAIR_EAM_KOKKOS_H
 
-#include <cstdio>
 #include "kokkos_base.h"
 #include "pair_kokkos.h"
 #include "pair_eam.h"
diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp
index 3a857a6485..8698687377 100644
--- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp
+++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp
@@ -15,20 +15,17 @@
    Contributing author: Stan Moore (Sandia)
 ------------------------------------------------------------------------- */
 
+#include "pair_exp6_rx_kokkos.h"
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_exp6_rx_kokkos.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neigh_list.h"
-#include "math_const.h"
 #include "math_special_kokkos.h"
 #include "memory_kokkos.h"
 #include "error.h"
-#include "modify.h"
 #include "fix.h"
 #include <cfloat>
 #include "atom_masks.h"
@@ -41,7 +38,6 @@
 #endif
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace MathSpecialKokkos;
 
 #define MAXLINE 1024
diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp
index 00df4a8f3c..b5b0a9d02b 100644
--- a/src/KOKKOS/pair_hybrid_kokkos.cpp
+++ b/src/KOKKOS/pair_hybrid_kokkos.cpp
@@ -11,20 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
-#include <cctype>
 #include "pair_hybrid_kokkos.h"
+#include <cstring>
 #include "atom_kokkos.h"
 #include "force.h"
 #include "pair.h"
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "comm.h"
 #include "memory_kokkos.h"
-#include "error.h"
 #include "respa.h"
 #include "atom_masks.h"
 #include "kokkos.h"
diff --git a/src/KOKKOS/pair_hybrid_kokkos.h b/src/KOKKOS/pair_hybrid_kokkos.h
index 94e034f875..799354cf01 100644
--- a/src/KOKKOS/pair_hybrid_kokkos.h
+++ b/src/KOKKOS/pair_hybrid_kokkos.h
@@ -20,7 +20,6 @@ PairStyle(hybrid/kk,PairHybridKokkos)
 #ifndef LMP_PAIR_HYBRID_KOKKOS_H
 #define LMP_PAIR_HYBRID_KOKKOS_H
 
-#include <cstdio>
 #include "pair_hybrid.h"
 #include "pair_kokkos.h"
 #include "kokkos_type.h"
diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp
index a2c3edab65..0cebd79c88 100644
--- a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp
+++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp
@@ -11,14 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
+#include "pair_hybrid_overlay_kokkos.h"
 #include <cstring>
 #include <cctype>
-#include "pair_hybrid_overlay_kokkos.h"
 #include "atom.h"
 #include "force.h"
-#include "neighbor.h"
-#include "neigh_request.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
index 510740112a..ae6cb61b60 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
@@ -15,28 +15,21 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_charmm_coul_charmm_implicit_kokkos.h"
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
index 51c96354f9..9cdef267e2 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
@@ -15,28 +15,22 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_charmm_coul_charmm_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
index 22faa98935..441070248d 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
@@ -15,28 +15,22 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_charmm_coul_long_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
index 60d480188b..1f7642e965 100644
--- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
@@ -11,11 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_class2_coul_cut_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
 #include "comm.h"
@@ -24,15 +22,12 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
index 4c8aea8e92..c88ff9378e 100644
--- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
@@ -11,28 +11,22 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_class2_coul_long_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp
index dd42baa4e0..9900e7361f 100644
--- a/src/KOKKOS/pair_lj_class2_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp
@@ -15,28 +15,22 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_class2_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
index cb5ab96871..1601e4a4b2 100644
--- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
@@ -11,28 +11,22 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_coul_cut_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
index 800092a09b..6e7d1eeb8b 100644
--- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
@@ -15,28 +15,22 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_coul_debye_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
index f793485b47..b7dc7cc26d 100644
--- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
@@ -15,20 +15,16 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_coul_dsf_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "math_const.h"
 #include "memory_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
index 02150586f4..122d59af82 100644
--- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
@@ -11,20 +11,16 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_coul_long_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "math_const.h"
 #include "memory_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp
index 4ba8c00f88..df750b7524 100644
--- a/src/KOKKOS/pair_lj_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp
@@ -11,28 +11,21 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_kokkos.h"
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp
index 5ea6c9e438..38bebc364f 100644
--- a/src/KOKKOS/pair_lj_expand_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp
@@ -15,28 +15,22 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_expand_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
index 2421d059da..a46a5c0441 100644
--- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
@@ -15,28 +15,22 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_gromacs_coul_gromacs_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
index 09a0261ae1..23ed5e5595 100644
--- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
@@ -15,28 +15,22 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_gromacs_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp
index c2375fa7a8..25f081d255 100644
--- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp
@@ -11,22 +11,18 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_sdk_kokkos.h"
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
 #include <cstring>
-#include "pair_lj_sdk_kokkos.h"
 #include "kokkos.h"
 #include "atom_kokkos.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
@@ -34,7 +30,6 @@
 #include "lj_sdk_common.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace LJSDKParms;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp
index b308330ead..d3e3042a34 100644
--- a/src/KOKKOS/pair_morse_kokkos.cpp
+++ b/src/KOKKOS/pair_morse_kokkos.cpp
@@ -15,20 +15,16 @@
    Contributing authors: Stefan Paquay (Eindhoven University of Technology)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_morse_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "math_const.h"
 #include "memory_kokkos.h"
diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp
index 7d17ac3f43..75247859ed 100644
--- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp
+++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp
@@ -21,21 +21,16 @@
    The Journal of Chemical Physics, 2016, 144, 104501.
 ------------------------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cmath>
-#include "math_const.h"
-#include <cstdlib>
-#include <cstring>
 #include "pair_multi_lucy_rx_kokkos.h"
+#include <cmath>
+#include <cstring>
+#include "math_const.h"
 #include "atom_kokkos.h"
 #include "force.h"
 #include "comm.h"
 #include "neigh_list.h"
 #include "memory_kokkos.h"
 #include "error.h"
-#include "citeme.h"
-#include "modify.h"
-#include "fix.h"
 #include "atom_masks.h"
 #include "neigh_request.h"
 #include "kokkos.h"
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index 64651be270..d0ad1f1b09 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -15,11 +15,10 @@
    Contributing author: Ray Shan (SNL), Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_reaxc_kokkos.h"
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_reaxc_kokkos.h"
 #include "kokkos.h"
 #include "atom_kokkos.h"
 #include "comm.h"
@@ -27,9 +26,6 @@
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "neigh_list_kokkos.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
 #include "math_const.h"
 #include "math_special.h"
 #include "memory_kokkos.h"
@@ -38,7 +34,6 @@
 #include "reaxc_defs.h"
 #include "reaxc_lookup.h"
 #include "reaxc_tool_box.h"
-#include "modify.h"
 
 
 #define TEAMSIZE 128
diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h
index 89dfc4d884..783ea33c4e 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.h
+++ b/src/KOKKOS/pair_reaxc_kokkos.h
@@ -23,7 +23,6 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos<LMPHostType>)
 #ifndef LMP_PAIR_REAXC_KOKKOS_H
 #define LMP_PAIR_REAXC_KOKKOS_H
 
-#include <cstdio>
 #include "pair_kokkos.h"
 #include "pair_reaxc.h"
 #include "neigh_list_kokkos.h"
diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp
index da4737a2c1..e85afa362f 100644
--- a/src/KOKKOS/pair_sw_kokkos.cpp
+++ b/src/KOKKOS/pair_sw_kokkos.cpp
@@ -15,11 +15,8 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_sw_kokkos.h"
+#include <cmath>
 #include "kokkos.h"
 #include "pair_kokkos.h"
 #include "atom_kokkos.h"
@@ -30,7 +27,6 @@
 #include "memory_kokkos.h"
 #include "neighbor.h"
 #include "neigh_list_kokkos.h"
-#include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 #include "math_const.h"
diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp
index 737d600d1e..5ee24ad479 100644
--- a/src/KOKKOS/pair_table_kokkos.cpp
+++ b/src/KOKKOS/pair_table_kokkos.cpp
@@ -15,15 +15,11 @@
    Contributing author: Christian Trott (SNL)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "pair_table_kokkos.h"
+#include <cstring>
 #include "kokkos.h"
 #include "atom.h"
 #include "force.h"
-#include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp
index ec7a2ffb94..daebeda8db 100644
--- a/src/KOKKOS/pair_table_rx_kokkos.cpp
+++ b/src/KOKKOS/pair_table_rx_kokkos.cpp
@@ -15,11 +15,10 @@
    Contributing author: Dan Ibanez (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_table_rx_kokkos.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "pair_table_rx_kokkos.h"
 #include "kokkos.h"
 #include "atom.h"
 #include "force.h"
diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp
index 9252e3de52..b360b20ef3 100644
--- a/src/KOKKOS/pair_tersoff_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_kokkos.cpp
@@ -15,11 +15,8 @@
    Contributing author: Ray Shan (SNL) and Christian Trott (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_tersoff_kokkos.h"
+#include <cmath>
 #include "kokkos.h"
 #include "atom_kokkos.h"
 #include "comm.h"
@@ -27,9 +24,6 @@
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "neigh_list_kokkos.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
 #include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h
index f73d4fe2d8..7d41fe2346 100644
--- a/src/KOKKOS/pair_tersoff_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_kokkos.h
@@ -23,7 +23,6 @@ PairStyle(tersoff/kk/host,PairTersoffKokkos<LMPHostType>)
 #ifndef LMP_PAIR_TERSOFF_KOKKOS_H
 #define LMP_PAIR_TERSOFF_KOKKOS_H
 
-#include <cstdio>
 #include "pair_kokkos.h"
 #include "pair_tersoff.h"
 #include "neigh_list_kokkos.h"
diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
index 585074b128..81ef486999 100644
--- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
@@ -15,11 +15,8 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_tersoff_mod_kokkos.h"
+#include <cmath>
 #include "kokkos.h"
 #include "atom_kokkos.h"
 #include "comm.h"
@@ -27,9 +24,6 @@
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "neigh_list_kokkos.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
 #include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.h b/src/KOKKOS/pair_tersoff_mod_kokkos.h
index d7c94ffc93..889e1eadfa 100644
--- a/src/KOKKOS/pair_tersoff_mod_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_mod_kokkos.h
@@ -23,7 +23,6 @@ PairStyle(tersoff/mod/kk/host,PairTersoffMODKokkos<LMPHostType>)
 #ifndef LMP_PAIR_TERSOFF_MOD_KOKKOS_H
 #define LMP_PAIR_TERSOFF_MOD_KOKKOS_H
 
-#include <cstdio>
 #include "pair_kokkos.h"
 #include "pair_tersoff_mod.h"
 #include "neigh_list_kokkos.h"
diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
index e1e2211ab5..4593f32e36 100644
--- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
@@ -15,11 +15,9 @@
    Contributing author: Ray Shan (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_tersoff_zbl_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "atom_kokkos.h"
 #include "comm.h"
@@ -28,8 +26,6 @@
 #include "neigh_request.h"
 #include "neigh_list_kokkos.h"
 #include "update.h"
-#include "integrate.h"
-#include "respa.h"
 #include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.h b/src/KOKKOS/pair_tersoff_zbl_kokkos.h
index 3af4e0d8eb..0c7fa2e963 100644
--- a/src/KOKKOS/pair_tersoff_zbl_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.h
@@ -23,7 +23,6 @@ PairStyle(tersoff/zbl/kk/host,PairTersoffZBLKokkos<LMPHostType>)
 #ifndef LMP_PAIR_TERSOFF_ZBL_KOKKOS_H
 #define LMP_PAIR_TERSOFF_ZBL_KOKKOS_H
 
-#include <cstdio>
 #include "pair_kokkos.h"
 #include "pair_tersoff_zbl.h"
 #include "neigh_list_kokkos.h"
diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp
index 4a1f291b17..614d3334d5 100644
--- a/src/KOKKOS/pair_vashishta_kokkos.cpp
+++ b/src/KOKKOS/pair_vashishta_kokkos.cpp
@@ -15,11 +15,9 @@
    Contributing author: Anders Hafreager (UiO), andershaf@gmail.com
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_vashishta_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "kokkos.h"
 #include "pair_kokkos.h"
 #include "atom_kokkos.h"
@@ -28,9 +26,7 @@
 #include "force.h"
 #include "comm.h"
 #include "memory_kokkos.h"
-#include "neighbor.h"
 #include "neigh_list_kokkos.h"
-#include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 #include "math_const.h"
diff --git a/src/KOKKOS/pair_yukawa_kokkos.cpp b/src/KOKKOS/pair_yukawa_kokkos.cpp
index 27e18533a2..6dfffd4a54 100644
--- a/src/KOKKOS/pair_yukawa_kokkos.cpp
+++ b/src/KOKKOS/pair_yukawa_kokkos.cpp
@@ -14,26 +14,22 @@
 /* ----------------------------------------------------------------------
    Contributing authors: Stefan Paquay (Brandeis University)
 ------------------------------------------------------------------------- */
-#include <cmath>
-#include <cstdlib>
+
 #include "pair_yukawa_kokkos.h"
+#include <cmath>
 #include "kokkos.h"
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define KOKKOS_CUDA_MAX_THREADS 256
 #define KOKKOS_CUDA_MIN_BLOCKS 8
diff --git a/src/KOKKOS/pair_zbl_kokkos.cpp b/src/KOKKOS/pair_zbl_kokkos.cpp
index 06c84e5189..5697dd5b00 100644
--- a/src/KOKKOS/pair_zbl_kokkos.cpp
+++ b/src/KOKKOS/pair_zbl_kokkos.cpp
@@ -15,21 +15,16 @@
    Contributing authors: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_zbl_kokkos.h"
+#include <cmath>
+#include <cstring>
 #include "atom_kokkos.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
-#include "math_const.h"
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
@@ -39,7 +34,6 @@
 // "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985.
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace PairZBLConstants;
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp
index 0d45f866b4..fa5687b90c 100644
--- a/src/KOKKOS/pppm_kokkos.cpp
+++ b/src/KOKKOS/pppm_kokkos.cpp
@@ -15,20 +15,15 @@
    Contributing author: Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
-#include <cstdio>
-#include <cstdlib>
-#include <cmath>
 #include "pppm_kokkos.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom_kokkos.h"
 #include "comm.h"
 #include "gridcomm_kokkos.h"
 #include "neighbor.h"
 #include "force.h"
 #include "pair.h"
-#include "bond.h"
-#include "angle.h"
 #include "domain.h"
 #include "fft3d_kokkos.h"
 #include "remap_kokkos.h"
diff --git a/src/KOKKOS/rand_pool_wrap_kokkos.cpp b/src/KOKKOS/rand_pool_wrap_kokkos.cpp
index 51ebcb154e..2d8865feb0 100644
--- a/src/KOKKOS/rand_pool_wrap_kokkos.cpp
+++ b/src/KOKKOS/rand_pool_wrap_kokkos.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "comm.h"
 #include "rand_pool_wrap_kokkos.h"
+#include "comm.h"
 #include "lammps.h"
 #include "kokkos.h"
 #include "random_mars.h"
diff --git a/src/KOKKOS/region_block_kokkos.cpp b/src/KOKKOS/region_block_kokkos.cpp
index 730ef81466..b28230290e 100644
--- a/src/KOKKOS/region_block_kokkos.cpp
+++ b/src/KOKKOS/region_block_kokkos.cpp
@@ -11,11 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "region_block_kokkos.h"
-#include "domain.h"
-#include "force.h"
 #include "atom_kokkos.h"
 #include "atom_masks.h"
 
diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp
index b80d5e0646..23952b71d8 100644
--- a/src/KOKKOS/verlet_kokkos.cpp
+++ b/src/KOKKOS/verlet_kokkos.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "verlet_kokkos.h"
 #include "neighbor.h"
 #include "domain.h"
 #include "comm.h"
-#include "atom.h"
 #include "atom_kokkos.h"
 #include "atom_masks.h"
 #include "force.h"
@@ -29,15 +27,10 @@
 #include "output.h"
 #include "update.h"
 #include "modify.h"
-#include "compute.h"
-#include "fix.h"
 #include "timer.h"
 #include "memory_kokkos.h"
-#include "error.h"
 #include "kokkos.h"
 
-#include <ctime>
-
 using namespace LAMMPS_NS;
 
 template<class ViewA, class ViewB>
@@ -150,7 +143,6 @@ void VerletKokkos::setup(int flag)
   }
   else if (force->pair) force->pair->compute_dummy(eflag,vflag);
 
-
   if (atomKK->molecular) {
     if (force->bond) {
       atomKK->sync(force->bond->execution_space,force->bond->datamask_read);
@@ -255,7 +247,6 @@ void VerletKokkos::setup_minimal(int flag)
   }
   else if (force->pair) force->pair->compute_dummy(eflag,vflag);
 
-
   if (atomKK->molecular) {
     if (force->bond) {
       atomKK->sync(force->bond->execution_space,force->bond->datamask_read);
@@ -292,7 +283,9 @@ void VerletKokkos::setup_minimal(int flag)
 
   if (force->newton) comm->reverse_comm();
 
+  lmp->kokkos->auto_sync = 0;
   modify->setup(vflag);
+  lmp->kokkos->auto_sync = 1;
   update->setupflag = 0;
 }
 
diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp
index ccbb3ed708..d74d90b0d6 100644
--- a/src/KSPACE/ewald.cpp
+++ b/src/KSPACE/ewald.cpp
@@ -18,12 +18,9 @@
      triclinic added by Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
-#include <cstdio>
-#include <cstring>
-#include <cmath>
 #include "ewald.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/KSPACE/ewald_dipole.cpp b/src/KSPACE/ewald_dipole.cpp
index 89ef7e39a8..c3442beef5 100644
--- a/src/KSPACE/ewald_dipole.cpp
+++ b/src/KSPACE/ewald_dipole.cpp
@@ -15,12 +15,10 @@
    Contributing authors: Julien Tranchida (SNL), Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "ewald_dipole.h"
 #include <mpi.h>
-#include <cstdlib>
-#include <cstdio>
 #include <cstring>
 #include <cmath>
-#include "ewald_dipole.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -32,9 +30,6 @@
 #include "error.h"
 #include "update.h"
 
-#include "math_const.h"
-#include "math_special.h"
-
 using namespace LAMMPS_NS;
 using namespace MathConst;
 using namespace MathSpecial;
diff --git a/src/KSPACE/ewald_dipole_spin.cpp b/src/KSPACE/ewald_dipole_spin.cpp
index 698203c85c..e7d67680a1 100644
--- a/src/KSPACE/ewald_dipole_spin.cpp
+++ b/src/KSPACE/ewald_dipole_spin.cpp
@@ -15,29 +15,22 @@
    Contributing authors: Julien Tranchida (SNL)
 ------------------------------------------------------------------------- */
 
+#include "ewald_dipole_spin.h"
 #include <mpi.h>
-#include <cstdlib>
-#include <cstdio>
 #include <cstring>
 #include <cmath>
-#include "ewald_dipole_spin.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "pair.h"
 #include "domain.h"
 #include "math_const.h"
-#include "math_special.h"
 #include "memory.h"
 #include "error.h"
 #include "update.h"
 
-#include "math_const.h"
-#include "math_special.h"
-
 using namespace LAMMPS_NS;
 using namespace MathConst;
-using namespace MathSpecial;
 
 #define SMALL 0.00001
 
diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp
index 0603d68eb2..a7ac66fdd3 100644
--- a/src/KSPACE/ewald_disp.cpp
+++ b/src/KSPACE/ewald_disp.cpp
@@ -15,12 +15,10 @@
    Contributing authors: Pieter in 't Veld (SNL), Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "ewald_disp.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdio>
-#include <cstdlib>
 #include <cmath>
-#include "ewald_disp.h"
 #include "math_vector.h"
 #include "math_const.h"
 #include "math_special.h"
diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp
index a0abd50c01..c9cf8df172 100644
--- a/src/KSPACE/fft3d.cpp
+++ b/src/KSPACE/fft3d.cpp
@@ -19,11 +19,11 @@
                          Paul Coffman (IBM) added MPI collectives remap
 ------------------------------------------------------------------------- */
 
+#include "fft3d.h"
 #include <mpi.h>
 #include <cstdio>
 #include <cstdlib>
 #include <cmath>
-#include "fft3d.h"
 #include "remap.h"
 #if defined(_OPENMP)
 #include <omp.h>
diff --git a/src/KSPACE/fft3d.h b/src/KSPACE/fft3d.h
index a51818d986..8c3d2f27ad 100644
--- a/src/KSPACE/fft3d.h
+++ b/src/KSPACE/fft3d.h
@@ -11,6 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include <mpi.h>
+
 // User-settable FFT precision
 
 // FFT_PRECISION = 1 is single-precision complex (4-byte real, 4-byte imag)
diff --git a/src/KSPACE/fft3d_wrap.cpp b/src/KSPACE/fft3d_wrap.cpp
index b9a6f0ae46..507b23d27d 100644
--- a/src/KSPACE/fft3d_wrap.cpp
+++ b/src/KSPACE/fft3d_wrap.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "fft3d_wrap.h"
+#include <mpi.h>
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp
index 0c726985dc..cfd88609b3 100644
--- a/src/KSPACE/fix_tune_kspace.cpp
+++ b/src/KSPACE/fix_tune_kspace.cpp
@@ -15,13 +15,11 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "fix_tune_kspace.h"
+#include <cmath>
+#include <cstring>
+#include <limits>
 #include "update.h"
-#include "domain.h"
-#include "atom.h"
-#include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "pair.h"
@@ -31,9 +29,6 @@
 #include "neighbor.h"
 #include "modify.h"
 #include "compute.h"
-#include <iostream>
-#include <cmath>
-#include <limits>
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
 #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a))
 #define GOLD 1.618034
@@ -101,7 +96,7 @@ void FixTuneKspace::init()
   double old_acc = force->kspace->accuracy/force->kspace->two_charge_force;
   char old_acc_str[16];
   snprintf(old_acc_str,16,"%g",old_acc);
-  strcpy(new_acc_str,old_acc_str);
+  strncpy(new_acc_str,old_acc_str,16);
 
   int itmp;
   double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp);
@@ -131,36 +126,37 @@ void FixTuneKspace::pre_exchange()
     // test Ewald
     store_old_kspace_settings();
     strcpy(new_kspace_style,"ewald");
-    sprintf(new_pair_style,"%s/long",base_pair_style);
+    snprintf(new_pair_style,64,"%s/long",base_pair_style);
     update_pair_style(new_pair_style,pair_cut_coul);
     update_kspace_style(new_kspace_style,new_acc_str);
   } else if (niter == 2) {
     // test PPPM
     store_old_kspace_settings();
     strcpy(new_kspace_style,"pppm");
-    sprintf(new_pair_style,"%s/long",base_pair_style);
+    snprintf(new_pair_style,64,"%s/long",base_pair_style);
     update_pair_style(new_pair_style,pair_cut_coul);
     update_kspace_style(new_kspace_style,new_acc_str);
   } else if (niter == 3) {
     // test MSM
     store_old_kspace_settings();
     strcpy(new_kspace_style,"msm");
-    sprintf(new_pair_style,"%s/msm",base_pair_style);
+    snprintf(new_pair_style,64,"%s/msm",base_pair_style);
     update_pair_style(new_pair_style,pair_cut_coul);
     update_kspace_style(new_kspace_style,new_acc_str);
   } else if (niter == 4) {
     store_old_kspace_settings();
-    cout << "ewald_time = " << ewald_time << endl;
-    cout << "pppm_time = " << pppm_time << endl;
-    cout << "msm_time = " << msm_time << endl;
+    if (screen) fprintf(screen,"ewald_time = %g\npppm_time = %g\nmsm_time = %g",
+                        ewald_time, pppm_time, msm_time);
+    if (logfile) fprintf(logfile,"ewald_time = %g\npppm_time = %g\nmsm_time = %g",
+                         ewald_time, pppm_time, msm_time);
     // switch to fastest one
     strcpy(new_kspace_style,"ewald");
-    sprintf(new_pair_style,"%s/long",base_pair_style);
+    snprintf(new_pair_style,64,"%s/long",base_pair_style);
     if (pppm_time < ewald_time && pppm_time < msm_time)
       strcpy(new_kspace_style,"pppm");
     else if (msm_time < pppm_time && msm_time < ewald_time) {
       strcpy(new_kspace_style,"msm");
-      sprintf(new_pair_style,"%s/msm",base_pair_style);
+      snprintf(new_pair_style,64,"%s/msm",base_pair_style);
     }
     update_pair_style(new_pair_style,pair_cut_coul);
     update_kspace_style(new_kspace_style,new_acc_str);
@@ -243,8 +239,8 @@ void FixTuneKspace::update_pair_style(char *new_pair_style,
   p_pair_settings_file = tmpfile();
   force->pair->write_restart(p_pair_settings_file);
   rewind(p_pair_settings_file);
-
-  cout << "Creating new pair style: " << new_pair_style << endl;
+  if (screen) fprintf(screen,"Creating new pair style: %s\n",new_pair_style);
+  if (logfile) fprintf(logfile,"Creating new pair style: %s\n",new_pair_style);
   // delete old pair style and create new one
   force->create_pair(new_pair_style,1);
 
@@ -253,7 +249,8 @@ void FixTuneKspace::update_pair_style(char *new_pair_style,
 
   double *pcutoff = (double *) force->pair->extract("cut_coul",itmp);
   double current_cutoff = *pcutoff;
-  cout << "Coulomb cutoff for real space: " << current_cutoff << endl;
+  if (screen) fprintf(screen,"Coulomb cutoff for real space: %g\n", current_cutoff);
+  if (logfile) fprintf(logfile,"Coulomb cutoff for real space: %g\n", current_cutoff);
 
   // close temporary file
   fclose(p_pair_settings_file);
@@ -321,7 +318,8 @@ void FixTuneKspace::adjust_rcut(double time)
   int itmp;
   double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp);
   double current_cutoff = *p_cutoff;
-  cout << "Old Coulomb cutoff for real space: " << current_cutoff << endl;
+  if (screen) fprintf(screen,"Old Coulomb cutoff for real space: %g\n",current_cutoff);
+  if (logfile) fprintf(logfile,"Old Coulomb cutoff for real space: %g\n",current_cutoff);
 
   // use Brent's method from Numerical Recipes to find optimal real space cutoff
 
@@ -391,7 +389,8 @@ void FixTuneKspace::adjust_rcut(double time)
   // report the new cutoff
   double *new_cutoff = (double *) force->pair->extract("cut_coul",itmp);
   current_cutoff = *new_cutoff;
-  cout << "Adjusted Coulomb cutoff for real space: " << current_cutoff << endl;
+  if (screen) fprintf(screen,"Adjusted Coulomb cutoff for real space: %g\n", current_cutoff);
+  if (logfile) fprintf(logfile,"Adjusted Coulomb cutoff for real space: %g\n", current_cutoff);
 
   store_old_kspace_settings();
   update_pair_style(new_pair_style,pair_cut_coul);
diff --git a/src/KSPACE/fix_tune_kspace.h b/src/KSPACE/fix_tune_kspace.h
index 6f40fc8711..1ccd735317 100644
--- a/src/KSPACE/fix_tune_kspace.h
+++ b/src/KSPACE/fix_tune_kspace.h
@@ -20,7 +20,6 @@ FixStyle(tune/kspace,FixTuneKspace)
 #ifndef LMP_FIX_TUNE_KSPACE_H
 #define LMP_FIX_TUNE_KSPACE_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
@@ -52,10 +51,10 @@ class FixTuneKspace : public Fix {
 
   double ewald_time,pppm_time,msm_time;
   double pair_cut_coul;
-  char new_acc_str[12];
-  char new_kspace_style[20];
-  char new_pair_style[20];
-  char base_pair_style[20];
+  char new_acc_str[16];
+  char new_kspace_style[64];
+  char new_pair_style[64];
+  char base_pair_style[64];
 
   int old_differentiation_flag;
   int old_slabflag;
diff --git a/src/KSPACE/gridcomm.cpp b/src/KSPACE/gridcomm.cpp
index ba08c9be26..368e7370fe 100644
--- a/src/KSPACE/gridcomm.cpp
+++ b/src/KSPACE/gridcomm.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "gridcomm.h"
-#include "comm.h"
+#include <mpi.h>
 #include "kspace.h"
 #include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp
index d7cc3f6876..81dbabdbbd 100644
--- a/src/KSPACE/msm.cpp
+++ b/src/KSPACE/msm.cpp
@@ -15,12 +15,10 @@
    Contributing authors: Paul Crozier, Stan Moore, Stephen Bond, (all SNL)
 ------------------------------------------------------------------------- */
 
+#include "msm.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdio>
-#include <cstdlib>
 #include <cmath>
-#include "msm.h"
 #include "atom.h"
 #include "comm.h"
 #include "gridcomm.h"
diff --git a/src/KSPACE/msm.h b/src/KSPACE/msm.h
index 0f81eb9c3f..bf393473e7 100644
--- a/src/KSPACE/msm.h
+++ b/src/KSPACE/msm.h
@@ -20,9 +20,6 @@ KSpaceStyle(msm,MSM)
 #ifndef LMP_MSM_H
 #define LMP_MSM_H
 
-#include "lmptype.h"
-#include <mpi.h>
-
 #include "kspace.h"
 
 namespace LAMMPS_NS {
diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp
index c7896db50c..9119d51878 100644
--- a/src/KSPACE/msm_cg.cpp
+++ b/src/KSPACE/msm_cg.cpp
@@ -15,10 +15,9 @@
    Contributing authors: Paul Crozier, Stan Moore, Stephen Bond, (all SNL)
 ------------------------------------------------------------------------- */
 
+#include "msm_cg.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "gridcomm.h"
@@ -27,12 +26,8 @@
 #include "force.h"
 #include "neighbor.h"
 #include "memory.h"
-#include "msm_cg.h"
-
-#include "math_const.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define OFFSET 16384
 #define SMALLQ 0.00001
diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp
index f12f5779d9..e248a24ef7 100644
--- a/src/KSPACE/pair_born_coul_long.cpp
+++ b/src/KSPACE/pair_born_coul_long.cpp
@@ -15,11 +15,9 @@
    Contributing author: Ahmed Ismail (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_born_coul_long.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/KSPACE/pair_born_coul_msm.cpp b/src/KSPACE/pair_born_coul_msm.cpp
index eaa1c116c1..7300cd92e0 100644
--- a/src/KSPACE/pair_born_coul_msm.cpp
+++ b/src/KSPACE/pair_born_coul_msm.cpp
@@ -15,23 +15,17 @@
    Contributing author: Stan Moore (SNL), Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_born_coul_msm.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
 #include "kspace.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp
index 0a1ec88da5..c97856fa3c 100644
--- a/src/KSPACE/pair_buck_coul_long.cpp
+++ b/src/KSPACE/pair_buck_coul_long.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_buck_coul_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/KSPACE/pair_buck_coul_msm.cpp b/src/KSPACE/pair_buck_coul_msm.cpp
index 257d1b661f..1355a2f13a 100644
--- a/src/KSPACE/pair_buck_coul_msm.cpp
+++ b/src/KSPACE/pair_buck_coul_msm.cpp
@@ -11,23 +11,17 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_buck_coul_msm.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
 #include "kspace.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp
index c7a4a4b2f6..8127cbc127 100644
--- a/src/KSPACE/pair_buck_long_coul_long.cpp
+++ b/src/KSPACE/pair_buck_long_coul_long.cpp
@@ -15,12 +15,11 @@
    Contributing author: Pieter J. in 't Veld (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_buck_long_coul_long.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "math_vector.h"
-#include "pair_buck_long_coul_long.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
@@ -29,7 +28,6 @@
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp
index ae268b9857..7cedf3d003 100644
--- a/src/KSPACE/pair_coul_long.cpp
+++ b/src/KSPACE/pair_coul_long.cpp
@@ -15,20 +15,16 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp
index 960505142c..5d42e1f046 100644
--- a/src/KSPACE/pair_coul_msm.cpp
+++ b/src/KSPACE/pair_coul_msm.cpp
@@ -15,21 +15,13 @@
    Contributing authors: Stan Moore (SNL), Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_msm.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
 #include "kspace.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp
index b40eab244b..751ee77388 100644
--- a/src/KSPACE/pair_lj_charmm_coul_long.cpp
+++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp
@@ -15,17 +15,14 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_charmm_coul_long.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.cpp b/src/KSPACE/pair_lj_charmm_coul_msm.cpp
index 72a8e340bc..a93a1275f4 100644
--- a/src/KSPACE/pair_lj_charmm_coul_msm.cpp
+++ b/src/KSPACE/pair_lj_charmm_coul_msm.cpp
@@ -15,21 +15,13 @@
    Contributing authors: Paul Crozier (SNL), Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_charmm_coul_msm.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
 #include "kspace.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
index cdde211157..494a349768 100644
--- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
+++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
@@ -19,18 +19,14 @@
      additional assistance from Robert A. Latour, Clemson University
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_charmmfsw_coul_long.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "update.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp
index fde7fa8e35..fb79451b37 100644
--- a/src/KSPACE/pair_lj_cut_coul_long.cpp
+++ b/src/KSPACE/pair_lj_cut_coul_long.cpp
@@ -15,17 +15,15 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_coul_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp
index c2e566a117..4ebbcb9a3f 100644
--- a/src/KSPACE/pair_lj_cut_coul_msm.cpp
+++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp
@@ -15,27 +15,17 @@
    Contributing authors: Stan Moore (SNL), Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_coul_msm.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
 #include "kspace.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp
index f5889fd520..c98092f19b 100644
--- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp
+++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp
@@ -16,23 +16,18 @@
    simpler force assignment added by Rolf Isele-Holder (Aachen University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_tip4p_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "angle.h"
 #include "atom.h"
 #include "bond.h"
 #include "comm.h"
 #include "domain.h"
 #include "force.h"
-#include "kspace.h"
-#include "update.h"
-#include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp
index 493866a895..610fc4e89b 100644
--- a/src/KSPACE/pair_lj_long_coul_long.cpp
+++ b/src/KSPACE/pair_lj_long_coul_long.cpp
@@ -17,12 +17,11 @@
    University New Orleans)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_long_coul_long.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "math_vector.h"
-#include "pair_lj_long_coul_long.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
@@ -31,7 +30,6 @@
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp
index 3137b9d79a..08409dce72 100644
--- a/src/KSPACE/pair_lj_long_tip4p_long.cpp
+++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp
@@ -16,23 +16,18 @@
                          Rolf Isele-Holder (Aachen University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_long_tip4p_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "angle.h"
 #include "atom.h"
 #include "bond.h"
 #include "comm.h"
 #include "domain.h"
 #include "force.h"
-#include "kspace.h"
-#include "update.h"
-#include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp
index 9419fdf196..2c47f42beb 100644
--- a/src/KSPACE/pair_tip4p_long.cpp
+++ b/src/KSPACE/pair_tip4p_long.cpp
@@ -16,23 +16,18 @@
    simpler force assignment added by Rolf Isele-Holder (Aachen University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_tip4p_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "angle.h"
 #include "atom.h"
 #include "bond.h"
 #include "comm.h"
 #include "domain.h"
 #include "force.h"
-#include "kspace.h"
-#include "update.h"
-#include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp
index 1abb19e947..75470c962f 100644
--- a/src/KSPACE/pppm.cpp
+++ b/src/KSPACE/pppm.cpp
@@ -18,12 +18,10 @@
      triclinic added by Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pppm.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdio>
-#include <cstdlib>
 #include <cmath>
-#include "pppm.h"
 #include "atom.h"
 #include "comm.h"
 #include "gridcomm.h"
diff --git a/src/KSPACE/pppm.h b/src/KSPACE/pppm.h
index 6426b9c22d..11b98076d9 100644
--- a/src/KSPACE/pppm.h
+++ b/src/KSPACE/pppm.h
@@ -20,8 +20,7 @@ KSpaceStyle(pppm,PPPM)
 #ifndef LMP_PPPM_H
 #define LMP_PPPM_H
 
-#include "lmptype.h"
-#include <mpi.h>
+#include "kspace.h"
 
 #if defined(FFT_FFTW3)
 #define LMP_FFT_LIB "FFTW3"
@@ -42,8 +41,6 @@ typedef double FFT_SCALAR;
 #define MPI_FFT_SCALAR MPI_DOUBLE
 #endif
 
-#include "kspace.h"
-
 namespace LAMMPS_NS {
 
 class PPPM : public KSpace {
diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp
index 3285dba21c..bd23dedef1 100644
--- a/src/KSPACE/pppm_cg.cpp
+++ b/src/KSPACE/pppm_cg.cpp
@@ -15,11 +15,10 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
+#include "pppm_cg.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-
 #include "atom.h"
 #include "gridcomm.h"
 #include "domain.h"
@@ -27,9 +26,8 @@
 #include "force.h"
 #include "neighbor.h"
 #include "memory.h"
-#include "pppm_cg.h"
-
 #include "math_const.h"
+#include "remap.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp
index 21a777dd75..0eb761d9be 100644
--- a/src/KSPACE/pppm_dipole.cpp
+++ b/src/KSPACE/pppm_dipole.cpp
@@ -15,20 +15,15 @@
    Contributing authors: Stan Moore (SNL), Julien Tranchida (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pppm_dipole.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdio>
-#include <cstdlib>
 #include <cmath>
-#include "pppm_dipole.h"
 #include "atom.h"
 #include "comm.h"
 #include "gridcomm.h"
-#include "neighbor.h"
 #include "force.h"
 #include "pair.h"
-#include "bond.h"
-#include "angle.h"
 #include "domain.h"
 #include "fft3d_wrap.h"
 #include "remap_wrap.h"
diff --git a/src/KSPACE/pppm_dipole_spin.cpp b/src/KSPACE/pppm_dipole_spin.cpp
index 878d40c82e..9e9f07322c 100644
--- a/src/KSPACE/pppm_dipole_spin.cpp
+++ b/src/KSPACE/pppm_dipole_spin.cpp
@@ -15,33 +15,23 @@
    Contributing author: Julien Tranchida (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pppm_dipole_spin.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdio>
-#include <cstdlib>
-#include <cmath>
-#include "pppm_dipole_spin.h"
 #include "atom.h"
 #include "comm.h"
 #include "gridcomm.h"
-#include "neighbor.h"
 #include "force.h"
 #include "pair.h"
-#include "bond.h"
-#include "angle.h"
 #include "domain.h"
-#include "fft3d_wrap.h"
-#include "remap_wrap.h"
 #include "memory.h"
 #include "error.h"
 #include "update.h"
 
 #include "math_const.h"
-#include "math_special.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
-using namespace MathSpecial;
 
 #define MAXORDER 7
 #define OFFSET 16384
diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp
index ba0e85bbba..c30d55dd68 100644
--- a/src/KSPACE/pppm_disp.cpp
+++ b/src/KSPACE/pppm_disp.cpp
@@ -16,12 +16,10 @@
                          Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pppm_disp.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdio>
-#include <cstdlib>
 #include <cmath>
-#include "pppm_disp.h"
 #include "math_const.h"
 #include "atom.h"
 #include "comm.h"
diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h
index 8674669274..130671fa28 100644
--- a/src/KSPACE/pppm_disp.h
+++ b/src/KSPACE/pppm_disp.h
@@ -20,8 +20,7 @@ KSpaceStyle(pppm/disp,PPPMDisp)
 #ifndef LMP_PPPM_DISP_H
 #define LMP_PPPM_DISP_H
 
-#include "lmptype.h"
-#include <mpi.h>
+#include "kspace.h"
 
 #if defined(FFT_FFTW3)
 #define LMP_FFT_LIB "FFTW3"
@@ -41,8 +40,6 @@ typedef double FFT_SCALAR;
 #define MPI_FFT_SCALAR MPI_DOUBLE
 #endif
 
-#include "kspace.h"
-
 namespace LAMMPS_NS {
 
 
diff --git a/src/KSPACE/pppm_disp_tip4p.cpp b/src/KSPACE/pppm_disp_tip4p.cpp
index 2bc63a84bb..bc46152e2b 100644
--- a/src/KSPACE/pppm_disp_tip4p.cpp
+++ b/src/KSPACE/pppm_disp_tip4p.cpp
@@ -16,13 +16,12 @@
                          Rolf Isele-Holder (Aachen University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pppm_disp_tip4p.h"
+#include <cmath>
 #include "pppm_disp.h"
 #include "atom.h"
 #include "domain.h"
 #include "force.h"
-#include "memory.h"
 #include "error.h"
 #include "math_const.h"
 
diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp
index a5ed6de626..7b708d0355 100644
--- a/src/KSPACE/pppm_stagger.cpp
+++ b/src/KSPACE/pppm_stagger.cpp
@@ -15,15 +15,12 @@
    Contributing author: Stan Moore (Sandia)
 ------------------------------------------------------------------------- */
 
+#include "pppm_stagger.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdio>
-#include <cstdlib>
 #include <cmath>
-#include "pppm_stagger.h"
 #include "atom.h"
 #include "gridcomm.h"
-#include "force.h"
 #include "domain.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp
index b9fe3e6488..f664a0dca3 100644
--- a/src/KSPACE/pppm_tip4p.cpp
+++ b/src/KSPACE/pppm_tip4p.cpp
@@ -15,12 +15,12 @@
    Contributing authors: Amalie Frischknecht and Ahmed Ismail (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pppm_tip4p.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "domain.h"
 #include "force.h"
-#include "memory.h"
 #include "error.h"
 #include "math_const.h"
 
diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp
index 26541f121e..d4cfdea2b0 100644
--- a/src/KSPACE/remap.cpp
+++ b/src/KSPACE/remap.cpp
@@ -11,9 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "remap.h"
+#include <mpi.h>
 #include <cstdio>
 #include <cstdlib>
-#include "remap.h"
 
 #define PACK_DATA FFT_SCALAR
 
diff --git a/src/KSPACE/remap_wrap.cpp b/src/KSPACE/remap_wrap.cpp
index 8ea2918d7f..7929cd053c 100644
--- a/src/KSPACE/remap_wrap.cpp
+++ b/src/KSPACE/remap_wrap.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "remap_wrap.h"
+#include <mpi.h>
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp
index 645b298e09..7d4e89272d 100644
--- a/src/LATTE/fix_latte.cpp
+++ b/src/LATTE/fix_latte.cpp
@@ -15,9 +15,9 @@
    Contributing author: Christian Negre (LANL)
 ------------------------------------------------------------------------- */
 
+#include "fix_latte.h"
 #include <cstdio>
 #include <cstring>
-#include "fix_latte.h"
 #include "atom.h"
 #include "comm.h"
 #include "update.h"
diff --git a/src/MAKE/MACHINES/Makefile.astra_arm b/src/MAKE/MACHINES/Makefile.astra_arm
new file mode 100644
index 0000000000..3734208936
--- /dev/null
+++ b/src/MAKE/MACHINES/Makefile.astra_arm
@@ -0,0 +1,119 @@
+# astra_arm - ThunderX2 ARM/OpenMPI Based, use Arm-PL for FFTW
+
+# need to load the following modules:
+# 1) arm-based developer pack
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC =            mpicxx
+CCFLAGS =       -O3 -funroll-loops -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
+DEPFLAGS =      -M
+LINK =          mpicxx
+LINKFLAGS =     -O3 -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
+LIB =           -lstdc++
+ARCHIVE =       ar
+ARFLAGS =       -rcsv
+SIZE =          size
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings, all OPTIONAL
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings
+# see possible settings in Section 2.2 (step 4) of manual
+
+LMP_INC =       -DLAMMPS_GZIP
+
+# MPI library
+# see discussion in Section 2.2 (step 5) of manual
+# MPI wrapper compiler/linker can provide this info
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       
+MPI_PATH = 
+MPI_LIB =
+
+# FFT library
+# see discussion in Section 2.2 (step 6) of manaul
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC =    -DFFT_FFTW2 -armpl
+FFT_PATH =   
+FFT_LIB =     
+
+# JPEG and/or PNG library
+# see discussion in Section 2.2 (step 7) of manual
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =       
+JPG_PATH = 
+JPG_LIB =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# do not edit this section
+
+include	Makefile.package.settings
+include	Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
+EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE):	$(OBJ) $(EXTRA_LINK_DEPENDS)
+	$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+	$(SIZE) $(EXE)
+
+# Library targets
+
+lib:	$(OBJ) $(EXTRA_LINK_DEPENDS)
+	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib:	$(OBJ) $(EXTRA_LINK_DEPENDS)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+        $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+
+%.o:%.cpp $(EXTRA_CPP_DEPENDS)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp $(EXTRA_CPP_DEPENDS)
+	$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+%.o:%.cu $(EXTRA_CPP_DEPENDS)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+# Individual dependencies
+
+depend : fastdep.exe $(SRC)
+	@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
+
+fastdep.exe: ../DEPEND/fastdep.c
+	cc -O -o $@ $<
+
+sinclude .depend
diff --git a/src/MAKE/MACHINES/Makefile.astra_gcc b/src/MAKE/MACHINES/Makefile.astra_gcc
new file mode 100644
index 0000000000..3ee43800fc
--- /dev/null
+++ b/src/MAKE/MACHINES/Makefile.astra_gcc
@@ -0,0 +1,119 @@
+# astra-gcc - ThunderX2 GCC/OpenMPI Based, FFTW
+
+# need to load the following modules:
+# 1) arm-based developer pack
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC =            mpicxx
+CCFLAGS =       -O3 -funroll-loops -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
+DEPFLAGS =      -M
+LINK =          mpicxx
+LINKFLAGS =     -O3 -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
+LIB =           -lstdc++
+ARCHIVE =       ar
+ARFLAGS =       -rcsv
+SIZE =          size
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings, all OPTIONAL
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings
+# see possible settings in Section 2.2 (step 4) of manual
+
+LMP_INC =       -DLAMMPS_GZIP
+
+# MPI library
+# see discussion in Section 2.2 (step 5) of manual
+# MPI wrapper compiler/linker can provide this info
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       
+MPI_PATH = 
+MPI_LIB =
+
+# FFT library
+# see discussion in Section 2.2 (step 6) of manaul
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC =    -DFFT_FFTW2 -I${FFTW_INC}
+FFT_PATH =   -I${FFTW_INC}
+FFT_LIB =    -L${FFTW_LIB} -lfftw3
+
+# JPEG and/or PNG library
+# see discussion in Section 2.2 (step 7) of manual
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =       
+JPG_PATH = 
+JPG_LIB =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# do not edit this section
+
+include	Makefile.package.settings
+include	Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
+EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE):	$(OBJ) $(EXTRA_LINK_DEPENDS)
+	$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+	$(SIZE) $(EXE)
+
+# Library targets
+
+lib:	$(OBJ) $(EXTRA_LINK_DEPENDS)
+	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib:	$(OBJ) $(EXTRA_LINK_DEPENDS)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+        $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+
+%.o:%.cpp $(EXTRA_CPP_DEPENDS)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp $(EXTRA_CPP_DEPENDS)
+	$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+%.o:%.cu $(EXTRA_CPP_DEPENDS)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+# Individual dependencies
+
+depend : fastdep.exe $(SRC)
+	@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
+
+fastdep.exe: ../DEPEND/fastdep.c
+	cc -O -o $@ $<
+
+sinclude .depend
diff --git a/src/MAKE/MACHINES/Makefile.theta b/src/MAKE/MACHINES/Makefile.theta
index cad5a03b42..663f212020 100644
--- a/src/MAKE/MACHINES/Makefile.theta
+++ b/src/MAKE/MACHINES/Makefile.theta
@@ -1,7 +1,5 @@
-# knl = Flags for Knights Landing Xeon Phi Processor,Intel Compiler/MPI,MKL FFT
-# module load perftools-base perftools
+# theta = Flags for Knights Landing Xeon Phi Processor, Intel Compiler, Cray MPI, MKL FFT
 # make theta -j 8
-# pat_build -g mpi -u ./lmp_theta
 
 SHELL = /bin/sh
 
@@ -10,24 +8,16 @@ SHELL = /bin/sh
 # specify flags and libraries needed for your compiler
 
 CC =        CC -mkl
-#OPTFLAGS =       -O0
-OPTFLAGS =      -xMIC-AVX512 -O3 -fp-model fast=2 -no-prec-div -qoverride-limits
+OPTFLAGS =  -xMIC-AVX512 -O3 -fp-model fast=2 -no-prec-div -qoverride-limits
 CCFLAGS =   -g -qopenmp -DLAMMPS_MEMALIGN=64 -qno-offload \
                 -fno-alias -ansi-alias -restrict $(OPTFLAGS)
-#CCFLAGS +=      -DLMP_INTEL_NO_TBB
-#CCFLAGS +=      -DLAMMPS_BIGBIG
-#CCFLAGS +=      -D_USE_PAPI
-#CCFLAGS +=      -D_USE_CRAYPAT_API
+CCFLAGS +=  -std=c++11
 SHFLAGS =   -fPIC
 DEPFLAGS =  -M
 
 LINK =      $(CC)
-LINKFLAGS = -g -qopenmp $(OPTFLAGS)
-LINKFLAGS += -dynamic
-LIB =
-#LIB +=           -L${TBBROOT}/lib/intel64/gcc4.7 -ltbbmalloc
-LIB +=           -ltbbmalloc
-#LIB +=          /soft/debuggers/forge-7.0-2017-02-16/lib/64/libdmallocthcxx.a -zmuldefs
+LINKFLAGS = -g -qopenmp $(OPTFLAGS) -dynamic
+LIB =       -ltbbmalloc
 SIZE =      size
 
 ARCHIVE =   ar
@@ -99,35 +89,35 @@ vpath %.h ..
 # Link target
 
 $(EXE): $(OBJ)
-    $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
-    $(SIZE) $(EXE)
+	$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+	$(SIZE) $(EXE)
 
 # Library targets
 
 lib:    $(OBJ)
-    $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
 
 shlib:  $(OBJ)
-    $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
-        $(OBJ) $(EXTRA_LIB) $(LIB)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+	$(OBJ) $(EXTRA_LIB) $(LIB)
 
 # Compilation rules
 
 %.o:%.cpp
-    $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
 
 %.d:%.cpp
-    $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+	$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
 
 %.o:%.cu
-    $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
 
 # Individual dependencies
 
 depend : fastdep.exe $(SRC)
-    @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
+	@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
 
 fastdep.exe: ../DEPEND/fastdep.c
-    icc -O -o $@ $<
+	icc -O -o $@ $<
 
 sinclude .depend
diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu b/src/MAKE/OPTIONS/Makefile.intel_cpu
index 831b16d854..f8e5eb3797 100644
--- a/src/MAKE/OPTIONS/Makefile.intel_cpu
+++ b/src/MAKE/OPTIONS/Makefile.intel_cpu
@@ -10,7 +10,8 @@ CC =		mpiicpc
 OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
                 -qopt-zmm-usage=high
 CCFLAGS =	-qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
-                -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS)
+                -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
+                -I$(MKLROOT)/include
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
index 926518f354..2c363cb2bf 100644
--- a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
+++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
@@ -10,7 +10,8 @@ CC =		mpiicpc
 OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
                 -qopt-zmm-usage=high
 CCFLAGS =	-qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
-                -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS)
+                -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
+                -I$(MKLROOT)/include
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich b/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich
index 61934b69b4..a0730f3402 100644
--- a/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich
+++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich
@@ -10,7 +10,8 @@ CC =		mpicxx -cxx=icc
 OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
                 -qopt-zmm-usage=high
 CCFLAGS =	-qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
-                -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS)
+                -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
+                -I$(MKLROOT)/include
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi b/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi
index ee26443f7d..2e73bb2890 100644
--- a/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi
+++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi
@@ -11,7 +11,8 @@ CC =		mpicxx
 OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \
                 -qopt-zmm-usage=high
 CCFLAGS =	-qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
-                -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS)
+                -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
+                -I$(MKLROOT)/include
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
diff --git a/src/MAKE/OPTIONS/Makefile.knl b/src/MAKE/OPTIONS/Makefile.knl
index 8e266a4fce..cf7a3f8103 100644
--- a/src/MAKE/OPTIONS/Makefile.knl
+++ b/src/MAKE/OPTIONS/Makefile.knl
@@ -9,7 +9,8 @@ SHELL = /bin/sh
 CC =		mpiicpc
 OPTFLAGS =      -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
 CCFLAGS =	-qopenmp -qno-offload -fno-alias -ansi-alias -restrict \
-                -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS)
+                -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \
+                -I$(MKLROOT)/include
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp
index 5019e7711a..2f324bf097 100644
--- a/src/MANYBODY/fix_qeq_comb.cpp
+++ b/src/MANYBODY/fix_qeq_comb.cpp
@@ -15,16 +15,13 @@
    Contributing authors: Ray Shan (Sandia, tnshan@sandia.gov)
 ------------------------------------------------------------------------- */
 
+#include "fix_qeq_comb.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
 #include "pair_comb.h"
 #include "pair_comb3.h"
-#include "fix_qeq_comb.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/MANYBODY/fix_qeq_comb.h b/src/MANYBODY/fix_qeq_comb.h
index dd4c9f7290..c3a0ac08f3 100644
--- a/src/MANYBODY/fix_qeq_comb.h
+++ b/src/MANYBODY/fix_qeq_comb.h
@@ -20,7 +20,6 @@ FixStyle(qeq/comb,FixQEQComb)
 #ifndef LMP_FIX_QEQ_COMB_H
 #define LMP_FIX_QEQ_COMB_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp
index 68511b8709..64c778659c 100644
--- a/src/MANYBODY/pair_adp.cpp
+++ b/src/MANYBODY/pair_adp.cpp
@@ -16,11 +16,11 @@
                          Chandra Veer Singh (Cornell)
 ------------------------------------------------------------------------- */
 
+#include "pair_adp.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_adp.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index e3c5a1627b..fcc3a3efd2 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -20,28 +20,23 @@
      Thomas C. O'Connor (JHU) 2014
 ------------------------------------------------------------------------- */
 
+#include "pair_airebo.h"
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include <mpi.h>
-#include "pair_airebo.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "force.h"
 #include "comm.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "my_page.h"
-#include "math_const.h"
 #include "math_special.h"
 #include "memory.h"
 #include "error.h"
 #include "utils.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace MathSpecial;
 
 #define MAXLINE 1024
@@ -3198,6 +3193,7 @@ double PairAIREBO::piRCSpline(double Nij, double Nji, double Nijconj,
   dN3[0]=0.0;
   dN3[1]=0.0;
   dN3[2]=0.0;
+  piRC=0.0;
 
   if (typei==0 && typej==0) {
 
@@ -4348,70 +4344,70 @@ void PairAIREBO::Sptricubic_patch_coeffs(
 ) {
   const double C_inv[64][32] = {
     // output_matrix(2, 8*4, get_matrix(3))
-      1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,
-     -3,  3,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -2, -1,  0,  0,  0,  0,  0,  0,
-      2, -2,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  1,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -3,  3,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  2, -2,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-     -3,  0,  3,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -2,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -3,  0,  3,  0,  0,  0,  0,  0,
-      9, -9, -9,  9,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  6, -6,  3, -3,  0,  0,  0,  0,  6,  3, -6, -3,  0,  0,  0,  0,
-     -6,  6,  6, -6,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -4,  4, -2,  2,  0,  0,  0,  0, -3, -3,  3,  3,  0,  0,  0,  0,
-      2,  0, -2,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  2,  0, -2,  0,  0,  0,  0,  0,
-     -6,  6,  6, -6,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -3,  3, -3,  3,  0,  0,  0,  0, -4, -2,  4,  2,  0,  0,  0,  0,
-      4, -4, -4,  4,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  2, -2,  2, -2,  0,  0,  0,  0,  2,  2, -2, -2,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0, -3,  3,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  2, -2,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0, -3,  0,  3,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  9, -9, -9,  9,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0, -6,  6,  6, -6,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  2,  0, -2,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0, -6,  6,  6, -6,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  4, -4, -4,  4,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-     -3,  0,  0,  0,  3,  0,  0,  0, -2,  0,  0,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -3,  0,  0,  0,  3,  0,  0,  0,
-      9, -9,  0,  0, -9,  9,  0,  0,  6, -6,  0,  0,  3, -3,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  6,  3,  0,  0, -6, -3,  0,  0,
-     -6,  6,  0,  0,  6, -6,  0,  0, -4,  4,  0,  0, -2,  2,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -3, -3,  0,  0,  3,  3,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -3,  0,  0,  0,  3,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  9, -9,  0,  0, -9,  9,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -6,  6,  0,  0,  6, -6,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      9,  0, -9,  0, -9,  0,  9,  0,  6,  0, -6,  0,  3,  0, -3,  0,  6,  0,  3,  0, -6,  0, -3,  0,  0,  0,  0,  0,  0,  0,  0,  0,
-      0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  9,  0, -9,  0, -9,  0,  9,  0,
-    -27, 27, 27,-27, 27,-27,-27, 27,-18, 18, 18,-18, -9,  9,  9, -9,-18, 18, -9,  9, 18,-18,  9, -9,-18, -9, 18,  9, 18,  9,-18, -9,
-     18,-18,-18, 18,-18, 18, 18,-18, 12,-12,-12, 12,  6, -6, -6,  6, 12,-12,  6, -6,-12, 12, -6,  6,  9,  9, -9, -9, -9, -9,  9,  9,
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+    {-12,12, 12,-12, 12,-12,-12, 12, -6,  6,  6, -6, -6,  6,  6, -6, -8,  8, -4,  4,  8, -8,  4, -4, -6, -6,  6,  6,  6,  6, -6, -6},
+    { 4,  0, -4,  0, -4,  0,  4,  0,  2,  0, -2,  0,  2,  0, -2,  0,  2,  0,  2,  0, -2,  0, -2,  0,  0,  0,  0,  0,  0,  0,  0,  0},
+    { 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  4,  0, -4,  0, -4,  0,  4,  0},
+    {-12,12, 12,-12, 12,-12,-12, 12, -6,  6,  6, -6, -6,  6,  6, -6, -6,  6, -6,  6,  6, -6,  6, -6, -8, -4,  8,  4,  8,  4, -8, -4},
+    { 8, -8, -8,  8, -8,  8,  8, -8,  4, -4, -4,  4,  4, -4, -4,  4,  4, -4,  4, -4, -4,  4, -4,  4,  4,  4, -4, -4, -4, -4,  4,  4}
   };
   double dx = xmax - xmin;
   double dy = ymax - ymin;
@@ -4461,22 +4457,22 @@ void PairAIREBO::Spbicubic_patch_coeffs(
 ) {
   const double C_inv[16][12] = {
      // output_matrix(1, 4*3, get_matrix(2))
-      1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
-     -3, 3, 0, 0, 0, 0, 0, 0,-2,-1, 0, 0,
-      2,-2, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0,
-      0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
-      0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      0, 0, 0, 0,-3, 3, 0, 0, 0, 0, 0, 0,
-      0, 0, 0, 0, 2,-2, 0, 0, 0, 0, 0, 0,
-     -3, 0, 3, 0,-2, 0,-1, 0, 0, 0, 0, 0,
-      0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 3, 0,
-      9,-9,-9, 9, 6,-6, 3,-3, 6, 3,-6,-3,
-     -6, 6, 6,-6,-4, 4,-2, 2,-3,-3, 3, 3,
-      2, 0,-2, 0, 1, 0, 1, 0, 0, 0, 0, 0,
-      0, 0, 0, 0, 0, 0, 0, 0, 2, 0,-2, 0,
-     -6, 6, 6,-6,-3, 3,-3, 3,-4,-2, 4, 2,
-      4,-4,-4, 4, 2,-2, 2,-2, 2, 2,-2,-2,
+    { 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+    { 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0},
+    {-3, 3, 0, 0, 0, 0, 0, 0,-2,-1, 0, 0},
+    { 2,-2, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0},
+    { 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0},
+    { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+    { 0, 0, 0, 0,-3, 3, 0, 0, 0, 0, 0, 0},
+    { 0, 0, 0, 0, 2,-2, 0, 0, 0, 0, 0, 0},
+    {-3, 0, 3, 0,-2, 0,-1, 0, 0, 0, 0, 0},
+    { 0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 3, 0},
+    { 9,-9,-9, 9, 6,-6, 3,-3, 6, 3,-6,-3},
+    {-6, 6, 6,-6,-4, 4,-2, 2,-3,-3, 3, 3},
+    { 2, 0,-2, 0, 1, 0, 1, 0, 0, 0, 0, 0},
+    { 0, 0, 0, 0, 0, 0, 0, 0, 2, 0,-2, 0},
+    {-6, 6, 6,-6,-3, 3,-3, 3,-4,-2, 4, 2},
+    { 4,-4,-4, 4, 2,-2, 2,-2, 2, 2,-2,-2}
   };
   double dx = xmax - xmin;
   double dy = ymax - ymin;
diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h
index 8e92807afb..04d3fc399f 100644
--- a/src/MANYBODY/pair_airebo.h
+++ b/src/MANYBODY/pair_airebo.h
@@ -21,7 +21,6 @@ PairStyle(airebo,PairAIREBO)
 #define LMP_PAIR_AIREBO_H
 
 #include "pair.h"
-#include "my_page.h"
 #include <cmath>
 #include "math_const.h"
 
diff --git a/src/MANYBODY/pair_airebo_morse.cpp b/src/MANYBODY/pair_airebo_morse.cpp
index a39f7df82e..121f9557fd 100644
--- a/src/MANYBODY/pair_airebo_morse.cpp
+++ b/src/MANYBODY/pair_airebo_morse.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_airebo_morse.h"
-#include "force.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index c157e0763c..e604f44003 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -15,8 +15,9 @@
    Contributing author: Sergey Lishchuk
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_atm.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "citeme.h"
 #include "comm.h"
diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp
index 39f48cd05e..6b7468558e 100644
--- a/src/MANYBODY/pair_bop.cpp
+++ b/src/MANYBODY/pair_bop.cpp
@@ -32,24 +32,19 @@
    Rules"_http://lammps.sandia.gov/open_source.html
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <mpi.h>
 #include "pair_bop.h"
+#include <cmath>
+#include <cstring>
+#include <cctype>
+#include <mpi.h>
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "force.h"
 #include "comm.h"
-#include "domain.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
-#include <cctype>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h
index 3bd9b8cea9..eca0ec52b8 100644
--- a/src/MANYBODY/pair_bop.h
+++ b/src/MANYBODY/pair_bop.h
@@ -26,8 +26,6 @@ PairStyle(bop,PairBOP)
 #define LMP_PAIR_BOP_H
 
 #include "pair.h"
-#include <ctime>
-#include "update.h"
 
 namespace LAMMPS_NS {
 
@@ -44,20 +42,20 @@ class PairBOP : public Pair {
 
  private:
   int me;
-  int maxneigh;                    // maximum size of neighbor list on this processor
-  int maxneigh3;                    // maximum size of neighbor list on this processor
-  int update_list;                 // check for changing maximum size of neighbor list
-  int maxbopn;                     // maximum size of bop neighbor list for allocation
-  int maxnall;                     // maximum size of bop neighbor list for allocation
-  int *map;                        // mapping from atom types to elements
-  int nelements;                   // # of unique elments
-  int nr;                     // increments for the BOP pair potential
-  int ntheta;                     // increments for the angle function
-  int npower;                     // power of the angular function
-  int nBOt;                   // second BO increments
-  int bop_types;                   // number of elments in potential
-  int npairs;                      // number of element pairs
-  char **elements;                   // names of unique elements
+  int maxneigh;                 // maximum size of neighbor list on this processor
+  int maxneigh3;                // maximum size of neighbor list on this processor
+  int update_list;              // check for changing maximum size of neighbor list
+  int maxbopn;                  // maximum size of bop neighbor list for allocation
+  int maxnall;                  // maximum size of bop neighbor list for allocation
+  int *map;                     // mapping from atom types to elements
+  int nelements;                // # of unique elments
+  int nr;                       // increments for the BOP pair potential
+  int ntheta;                   // increments for the angle function
+  int npower;                   // power of the angular function
+  int nBOt;                     // second BO increments
+  int bop_types;                // number of elments in potential
+  int npairs;                   // number of element pairs
+  char **elements;              // names of unique elements
   int ***elem2param;
   int nparams;
   int bop_step;
@@ -66,23 +64,22 @@ class PairBOP : public Pair {
   int allocate_neigh;
   int nb_pi,nb_sg;
   int ago1;
-//  int cnt1;
 
-  int *BOP_index;                 // index for neighbor list position
-  int *BOP_total;                 // index for neighbor list position
-  int *BOP_index3;                 // index for neighbor list position
-  int *BOP_total3;                 // index for neighbor list position
-  int *neigh_index;                 // index for neighbor list position
-  int *neigh_index3;                 // index for neighbor list position
-  int neigh_total;                // total number of neighbors stored
-  int neigh_total3;                // total number of neighbors stored
-  int *cos_index;                 // index for neighbor cosine if not using on the fly
-  int *neigh_flag;                 // index for neighbor cosine if not using on the fly
-  int *neigh_flag3;                 // index for neighbor cosine if not using on the fly
-  int cos_total;                  // number of cosines stored if not using on the fly
-  int neigh_ct;                  //  limit for large arrays
+  int *BOP_index;               // index for neighbor list position
+  int *BOP_total;               // index for neighbor list position
+  int *BOP_index3;              // index for neighbor list position
+  int *BOP_total3;              // index for neighbor list position
+  int *neigh_index;             // index for neighbor list position
+  int *neigh_index3;            // index for neighbor list position
+  int neigh_total;              // total number of neighbors stored
+  int neigh_total3;             // total number of neighbors stored
+  int *cos_index;               // index for neighbor cosine if not using on the fly
+  int *neigh_flag;              // index for neighbor cosine if not using on the fly
+  int *neigh_flag3;             // index for neighbor cosine if not using on the fly
+  int cos_total;                // number of cosines stored if not using on the fly
+  int neigh_ct;                 // limit for large arrays
 
-/*Parameters variables*/
+  // Parameters variables
 
   int ncutoff,nfunc;
   int a_flag;
@@ -98,51 +95,50 @@ class PairBOP : public Pair {
   double beta3,rsmall,rbig,rcore;
   char **words;
 
-  double cutmax;                //max cutoff for all elements
-  int otfly;                        //Defines whether to do on the fly
-                                //calculations of angles and distances
-                                //on the fly will slow down calculations
-                                //but requires less memory on = 1, off=0
+  double cutmax;                // max cutoff for all elements
+  int otfly;                    // Defines whether to do on the fly
+                                // calculations of angles and distances
+                                // on the fly will slow down calculations
+                                // but requires less memory on = 1, off=0
 
-/* Neigh variables */
+  //  Neigh variables
 
   double *rcut,*rcut3,*dr,*rdr,*dr3,*rdr3;
   double *rcutsq,*rcutsq3;
   double **disij,*rij;
   double rcutall,rctroot;
 
-/*Triple variables */
+  // Triple variables
 
   double *cosAng,***dcosAng,***dcAng;
 
-/*Double variables */
+  // Double variables
 
   double *betaS,*dBetaS,*betaP;
   double *dBetaP,*repul,*dRepul;
 
-/*Sigma variables */
+  // Sigma variables
 
   int *itypeSigBk,nSigBk;
   double sigB,sigB_0;
   double sigB1;
 
-
-/*Pi variables */
+  // Pi variables
 
   int *itypePiBk,nPiBk;
   double piB,piB_0;
 
-/*Grids1 variables */
+  // Grids1 variables
 
   double **pBetaS,**pBetaS1,**pBetaS2,**pBetaS3;
   double **pBetaS4,**pBetaS5,**pBetaS6;
 
-/*Grids2 variables */
+  // Grids2 variables
 
   double **pBetaP,**pBetaP1,**pBetaP2,**pBetaP3;
   double **pBetaP4,**pBetaP5,**pBetaP6;
 
-/*Grids3 variables */
+  // Grids3 variables
 
   double **pRepul,**pRepul1,**pRepul2,**pRepul3;
   double **pRepul4,**pRepul5,**pRepul6;
@@ -155,13 +151,13 @@ class PairBOP : public Pair {
   double ****gfunc4,****gfunc5,****gfunc6;
   double dtheta,rdtheta;
 
-/*Grids4 variables */
+  // Grids4 variables
 
   double **FsigBO,**FsigBO1,**FsigBO2,**FsigBO3;
   double **FsigBO4,**FsigBO5,**FsigBO6;
   double dBO,rdBO;
 
-/* End of BOP variables */
+  // End of BOP variables
 
   double **rcmin,**rcmax,**rcmaxp;
   struct B_PI{
@@ -211,14 +207,6 @@ class PairBOP : public Pair {
   void memory_theta_destroy();
   void memory_theta_grow();
   double cutoff(double, double, int, double);
-/*
-  double betaSfunc(int, double);
-  double dBetaSfunc(int, double, double, double);
-  double betaPfunc(int, double);
-  double dBetaPfunc(int, double, double, double);
-  double repulfunc(int, double);
-  double dRepulfunc(int, double, double, double);
-*/
 
   void read_table(char *);
   void allocate();
@@ -229,9 +217,7 @@ class PairBOP : public Pair {
   void grow_pi(int,int);
   void grow_sigma(int,int);
 };
-
 }
-
 #endif
 #endif
 
diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp
index 980aa84b2a..2fc4caec7b 100644
--- a/src/MANYBODY/pair_comb.cpp
+++ b/src/MANYBODY/pair_comb.cpp
@@ -18,11 +18,11 @@
    and Aidan Thompson's Tersoff code in LAMMPS
 ------------------------------------------------------------------------- */
 
+#include "pair_comb.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_comb.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -30,7 +30,6 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "group.h"
-#include "update.h"
 #include "my_page.h"
 #include "math_const.h"
 #include "memory.h"
diff --git a/src/MANYBODY/pair_comb.h b/src/MANYBODY/pair_comb.h
index c798d5f347..19788dfab1 100644
--- a/src/MANYBODY/pair_comb.h
+++ b/src/MANYBODY/pair_comb.h
@@ -21,7 +21,6 @@ PairStyle(comb,PairComb)
 #define LMP_PAIR_COMB_H
 
 #include "pair.h"
-#include "my_page.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index 097f235ff2..6f1732dbb7 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -17,19 +17,19 @@
                       Dundar Yilmaz (dundar.yilmaz@zirve.edu.tr)
 ------------------------------------------------------------------------- */
 
+#include "pair_comb3.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_comb3.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
+#include "my_page.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "group.h"
-#include "update.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/MANYBODY/pair_comb3.h b/src/MANYBODY/pair_comb3.h
index 5d7e5d6beb..210f843139 100644
--- a/src/MANYBODY/pair_comb3.h
+++ b/src/MANYBODY/pair_comb3.h
@@ -21,7 +21,6 @@ PairStyle(comb3,PairComb3)
 #define LMP_PAIR_COMB3_H
 
 #include "pair.h"
-#include "my_page.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index b7957349b6..acb0e654d8 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/src/MANYBODY/pair_eam.cpp
@@ -15,11 +15,11 @@
    Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_eam.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_eam.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h
index 234552157b..8bcb44c347 100644
--- a/src/MANYBODY/pair_eam.h
+++ b/src/MANYBODY/pair_eam.h
@@ -20,7 +20,6 @@ PairStyle(eam,PairEAM)
 #ifndef LMP_PAIR_EAM_H
 #define LMP_PAIR_EAM_H
 
-#include <cstdio>
 #include "pair.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp
index c004030240..5b7f9877d7 100644
--- a/src/MANYBODY/pair_eam_alloy.cpp
+++ b/src/MANYBODY/pair_eam_alloy.cpp
@@ -15,10 +15,9 @@
    Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_eam_alloy.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp
index c111c6d950..28004eae7f 100644
--- a/src/MANYBODY/pair_eam_cd.cpp
+++ b/src/MANYBODY/pair_eam_cd.cpp
@@ -17,15 +17,14 @@
                         Germany Department of Materials Science
 ------------------------------------------------------------------------- */
 
+#include "pair_eam_cd.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_eam_cd.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp
index bbda84fdf1..7e00783922 100644
--- a/src/MANYBODY/pair_eam_fs.cpp
+++ b/src/MANYBODY/pair_eam_fs.cpp
@@ -15,10 +15,9 @@
    Contributing authors: Tim Lau (MIT)
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_eam_fs.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp
index f1c028ef38..dd65d92cdd 100644
--- a/src/MANYBODY/pair_eim.cpp
+++ b/src/MANYBODY/pair_eim.cpp
@@ -15,11 +15,10 @@
    Contributing author: Xiaowang Zhou (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_eim.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h
index 50f9934c44..f9fb2d5a77 100644
--- a/src/MANYBODY/pair_eim.h
+++ b/src/MANYBODY/pair_eim.h
@@ -20,7 +20,6 @@ PairStyle(eim,PairEIM)
 #ifndef LMP_PAIR_EIM_H
 #define LMP_PAIR_EIM_H
 
-#include <cstdio>
 #include "pair.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp
index e4b74f7a29..667311812b 100644
--- a/src/MANYBODY/pair_gw.cpp
+++ b/src/MANYBODY/pair_gw.cpp
@@ -16,11 +16,11 @@
    based on PairTersoff by Aidan Thompson (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_gw.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_gw.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp
index f3dd1bc04b..d39bf53b99 100644
--- a/src/MANYBODY/pair_gw_zbl.cpp
+++ b/src/MANYBODY/pair_gw_zbl.cpp
@@ -16,16 +16,13 @@
    Based on PairTersoffZBL by Aidan Thompson (SNL) and David Farrell (NWU)
 ------------------------------------------------------------------------- */
 
+#include "pair_gw_zbl.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_gw_zbl.h"
 #include "atom.h"
 #include "update.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
 #include "force.h"
 #include "comm.h"
 #include "memory.h"
diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp
index 05cdea8055..873a675cd9 100644
--- a/src/MANYBODY/pair_lcbop.cpp
+++ b/src/MANYBODY/pair_lcbop.cpp
@@ -16,27 +16,21 @@
      based on pair_airebo by Ase Henry (MIT)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <mpi.h>
 #include "pair_lcbop.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
 #include "force.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "my_page.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define MAXLINE 1024
 #define TOL 1.0e-9
@@ -1099,19 +1093,6 @@ void PairLCBOP::read_file(char *filename)
    init coefficients for TF_conj
 ------------------------------------------------------------------------- */
 
-#include <iostream>
-#include <fstream>
-#include <functional>
-template< class function > void print_function( double x_0, double x_1, size_t n, function f, std::ostream &stream ) {
-  double dx = (x_1-x_0)/n;
-  for( double x=x_0; x<=x_1+0.0001; x+=dx ) {
-    double f_val, df;
-    f_val = f(x, &df);
-    stream << x << " " << f_val << "   " << df << std::endl;
-  }
-  stream << std::endl;
-}
-
 void PairLCBOP::spline_init() {
   for( size_t N_conj_ij=0; N_conj_ij<2; N_conj_ij++ ) // N_conj_ij
   for( size_t N_ij=0; N_ij<4-1; N_ij++ )
diff --git a/src/MANYBODY/pair_lcbop.h b/src/MANYBODY/pair_lcbop.h
index 0d7c7a51b1..c7a7fab46d 100644
--- a/src/MANYBODY/pair_lcbop.h
+++ b/src/MANYBODY/pair_lcbop.h
@@ -21,7 +21,6 @@ PairStyle(lcbop,PairLCBOP)
 #define LMP_PAIR_LCBOP_H
 
 #include "pair.h"
-#include "my_page.h"
 #include <cmath>
 #include "math_const.h"
 
diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp
index a61b403459..92456790cc 100644
--- a/src/MANYBODY/pair_nb3b_harmonic.cpp
+++ b/src/MANYBODY/pair_nb3b_harmonic.cpp
@@ -16,18 +16,16 @@
    (based on Stillinger-Weber pair style)
 ------------------------------------------------------------------------- */
 
+#include "pair_nb3b_harmonic.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_nb3b_harmonic.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "force.h"
 #include "comm.h"
-#include "memory.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp
index d3aca4e889..d3964b292c 100644
--- a/src/MANYBODY/pair_polymorphic.cpp
+++ b/src/MANYBODY/pair_polymorphic.cpp
@@ -16,11 +16,11 @@
    This modifies from pair_tersoff.cpp by Aidan Thompson (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_polymorphic.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_polymorphic.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
@@ -30,10 +30,7 @@
 #include "memory.h"
 #include "error.h"
 
-#include "math_const.h"
-
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define MAXLINE 1024
 #define DELTA 4
diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h
index 32f1c5414a..e7c3cd0d26 100644
--- a/src/MANYBODY/pair_polymorphic.h
+++ b/src/MANYBODY/pair_polymorphic.h
@@ -22,6 +22,7 @@ PairStyle(polymorphic,PairPolymorphic)
 
 #include "pair.h"
 #include <cmath>
+#include <cstring>
 
 namespace LAMMPS_NS {
 
diff --git a/src/MANYBODY/pair_rebo.cpp b/src/MANYBODY/pair_rebo.cpp
index e07a1b3495..06357d8368 100644
--- a/src/MANYBODY/pair_rebo.cpp
+++ b/src/MANYBODY/pair_rebo.cpp
@@ -26,7 +26,7 @@ PairREBO::PairREBO(LAMMPS *lmp) : PairAIREBO(lmp) {
    global settings
 ------------------------------------------------------------------------- */
 
-void PairREBO::settings(int narg, char **/*arg*/)
+void PairREBO::settings(int narg, char ** /* arg */)
 {
   if (narg != 0) error->all(FLERR,"Illegal pair_style command");
 
diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp
index 5a148fb152..f1d1a6fa9f 100644
--- a/src/MANYBODY/pair_sw.cpp
+++ b/src/MANYBODY/pair_sw.cpp
@@ -15,21 +15,19 @@
    Contributing author: Aidan Thompson (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_sw.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_sw.h"
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
-#include "force.h"
 #include "comm.h"
+#include "error.h"
+#include "force.h"
 #include "memory.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
+#include "neigh_request.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp
index 213b1037bb..5f53760e71 100644
--- a/src/MANYBODY/pair_tersoff.cpp
+++ b/src/MANYBODY/pair_tersoff.cpp
@@ -15,11 +15,11 @@
    Contributing author: Aidan Thompson (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_tersoff.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_tersoff.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
@@ -30,9 +30,11 @@
 #include "error.h"
 
 #include "math_const.h"
+#include "math_special.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
+using namespace MathSpecial;
 
 #define MAXLINE 1024
 #define DELTA 4
@@ -604,7 +606,7 @@ double PairTersoff::zeta(Param *param, double rsqij, double rsqik,
   costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
               delrij[2]*delrik[2]) / (rij*rik);
 
-  if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0);
+  if (param->powermint == 3) arg = cube(param->lam3 * (rij-rik));
   else arg = param->lam3 * (rij-rik);
 
   if (arg > 69.0776) ex_delr = 1.e30;
@@ -744,7 +746,7 @@ void PairTersoff::ters_zetaterm_d(double prefactor,
 
   fc = ters_fc(rik,param);
   dfc = ters_fc_d(rik,param);
-  if (param->powermint == 3) tmp = pow(param->lam3 * (rij-rik),3.0);
+  if (param->powermint == 3) tmp = cube(param->lam3 * (rij-rik));
   else tmp = param->lam3 * (rij-rik);
 
   if (tmp > 69.0776) ex_delr = 1.e30;
@@ -752,7 +754,7 @@ void PairTersoff::ters_zetaterm_d(double prefactor,
   else ex_delr = exp(tmp);
 
   if (param->powermint == 3)
-    ex_delr_d = 3.0*pow(param->lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
+    ex_delr_d = 3.0*cube(param->lam3) * square(rij-rik)*ex_delr;
   else ex_delr_d = param->lam3 * ex_delr;
 
   cos_theta = vec3_dot(rij_hat,rik_hat);
diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp
index e8fdecfe01..9d4bdb7fd0 100644
--- a/src/MANYBODY/pair_tersoff_mod.cpp
+++ b/src/MANYBODY/pair_tersoff_mod.cpp
@@ -16,24 +16,22 @@
                         Vitaly Dozhdikov (JIHT of RAS) - MOD addition
 ------------------------------------------------------------------------- */
 
+#include "pair_tersoff_mod.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_tersoff_mod.h"
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
 #include "force.h"
 #include "comm.h"
+#include "math_const.h"
+#include "math_special.h"
 #include "memory.h"
 #include "error.h"
 
-#include "math_const.h"
-
 using namespace LAMMPS_NS;
 using namespace MathConst;
+using namespace MathSpecial;
 
 #define MAXLINE 1024
 #define DELTA 4
@@ -245,7 +243,7 @@ double PairTersoffMOD::zeta(Param *param, double rsqij, double rsqik,
   costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
               delrij[2]*delrik[2]) / (rij*rik);
 
-  if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0);
+  if (param->powermint == 3) arg = cube(param->lam3 * (rij-rik));
   else arg = param->lam3 * (rij-rik);
 
   if (arg > 69.0776) ex_delr = 1.e30;
@@ -318,7 +316,7 @@ void PairTersoffMOD::ters_zetaterm_d(double prefactor,
 
   fc = ters_fc(rik,param);
   dfc = ters_fc_d(rik,param);
-  if (param->powermint == 3) tmp = pow(param->lam3 * (rij-rik),3.0);
+  if (param->powermint == 3) tmp = cube(param->lam3 * (rij-rik));
   else tmp = param->lam3 * (rij-rik);
 
   if (tmp > 69.0776) ex_delr = 1.e30;
@@ -326,7 +324,7 @@ void PairTersoffMOD::ters_zetaterm_d(double prefactor,
   else ex_delr = exp(tmp);
 
   if (param->powermint == 3)
-    ex_delr_d = 3.0*pow(param->lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
+    ex_delr_d = 3.0*cube(param->lam3) * square(rij-rik)*ex_delr;
   else ex_delr_d = param->lam3 * ex_delr;
 
   cos_theta = vec3_dot(rij_hat,rik_hat);
diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp
index 4a5904c106..6c2c4f4e7a 100644
--- a/src/MANYBODY/pair_tersoff_mod_c.cpp
+++ b/src/MANYBODY/pair_tersoff_mod_c.cpp
@@ -15,24 +15,18 @@
    Contributing author: Ganga P Purja Pun (George Mason University, Fairfax)
 ------------------------------------------------------------------------- */
 
+#include "pair_tersoff_mod_c.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_tersoff_mod_c.h"
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
 #include "force.h"
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
 
-#include "math_const.h"
-
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define MAXLINE 1024
 #define DELTA 4
diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp
index 353e3d2264..d5e3fb1b0f 100644
--- a/src/MANYBODY/pair_tersoff_zbl.cpp
+++ b/src/MANYBODY/pair_tersoff_zbl.cpp
@@ -16,24 +16,23 @@
                         David Farrell (NWU) - ZBL addition
 ------------------------------------------------------------------------- */
 
+#include "pair_tersoff_zbl.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_tersoff_zbl.h"
 #include "atom.h"
 #include "update.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
 #include "force.h"
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
-
 #include "math_const.h"
+#include "math_special.h"
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
+using namespace MathSpecial;
 
 #define MAXLINE 1024
 #define DELTA 4
@@ -229,7 +228,7 @@ void PairTersoffZBL::repulsive(Param *param, double rsq, double &fforce,
 
   // ZBL repulsive portion
 
-  double esq = pow(global_e,2.0);
+  double esq = square(global_e);
   double a_ij = (0.8854*global_a_0) /
     (pow(param->Z_i,0.23) + pow(param->Z_j,0.23));
   double premult = (param->Z_i * param->Z_j * esq)/(4.0*MY_PI*global_epsilon_0);
@@ -289,5 +288,5 @@ double PairTersoffZBL::F_fermi(double r, Param *param)
 double PairTersoffZBL::F_fermi_d(double r, Param *param)
 {
   return param->ZBLexpscale*exp(-param->ZBLexpscale*(r-param->ZBLcut)) /
-    pow(1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)),2.0);
+    square(1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)));
 }
diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp
index 3d4b1d900e..13b44c58a4 100644
--- a/src/MANYBODY/pair_vashishta.cpp
+++ b/src/MANYBODY/pair_vashishta.cpp
@@ -16,21 +16,19 @@
                          Aidan Thompson (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_vashishta.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_vashishta.h"
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
-#include "force.h"
 #include "comm.h"
+#include "error.h"
+#include "force.h"
 #include "memory.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
+#include "neigh_request.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp
index d4eaa59f1a..bf39183b9d 100644
--- a/src/MANYBODY/pair_vashishta_table.cpp
+++ b/src/MANYBODY/pair_vashishta_table.cpp
@@ -15,21 +15,14 @@
    Contributing author: Anders Hafreager (UiO), andershaf@gmail.com
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_vashishta_table.h"
+#include <cstdio>
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
+#include "error.h"
 #include "force.h"
 #include "comm.h"
 #include "memory.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp
index 7d817ffbb1..9a4a0b6a7f 100644
--- a/src/MC/fix_atom_swap.cpp
+++ b/src/MC/fix_atom_swap.cpp
@@ -16,14 +16,13 @@
                          Alexander Stukowski
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cfloat>
-#include <cstdlib>
-#include <cstring>
 #include "fix_atom_swap.h"
+#include <mpi.h>
+#include <cmath>
+#include <cctype>
+#include <cfloat>
+#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "atom_vec_hybrid.h"
 #include "update.h"
 #include "modify.h"
 #include "fix.h"
@@ -40,18 +39,12 @@
 #include "dihedral.h"
 #include "improper.h"
 #include "kspace.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
-#include "thermo.h"
-#include "output.h"
 #include "neighbor.h"
-#include <iostream>
 
-using namespace std;
 using namespace LAMMPS_NS;
 using namespace FixConst;
-using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/MC/fix_atom_swap.h b/src/MC/fix_atom_swap.h
index 19895704f1..a5ce89b16b 100644
--- a/src/MC/fix_atom_swap.h
+++ b/src/MC/fix_atom_swap.h
@@ -20,7 +20,6 @@ FixStyle(atom/swap,FixAtomSwap)
 #ifndef LMP_FIX_MCSWAP_H
 #define LMP_FIX_MCSWAP_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index 05edc0509e..2ff0e4126f 100644
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -11,19 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
+#include "fix_bond_break.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdlib>
-#include "fix_bond_break.h"
 #include "update.h"
 #include "respa.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "force.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "random_mars.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index e1dd18cb5b..3f63a22d60 100644
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -11,15 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
+#include "fix_bond_create.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdlib>
-#include "fix_bond_create.h"
 #include "update.h"
 #include "respa.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "force.h"
 #include "pair.h"
 #include "comm.h"
diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp
index 9a72667907..187c552416 100644
--- a/src/MC/fix_bond_swap.cpp
+++ b/src/MC/fix_bond_swap.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_bond_swap.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "pair.h"
@@ -23,7 +23,6 @@
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "group.h"
 #include "comm.h"
 #include "domain.h"
 #include "modify.h"
diff --git a/src/MC/fix_bond_swap.h b/src/MC/fix_bond_swap.h
index 0443144c23..d24159d807 100644
--- a/src/MC/fix_bond_swap.h
+++ b/src/MC/fix_bond_swap.h
@@ -21,7 +21,6 @@ FixStyle(bond/swap,FixBondSwap)
 #define LMP_FIX_BONDSWAP_H
 
 #include "fix.h"
-#include "pair.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index 7ab0879335..1050fd4712 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -15,13 +15,12 @@
    Contributing author: Paul Crozier, Aidan Thompson (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_gcmc.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
-#include "atom_vec_hybrid.h"
 #include "molecule.h"
 #include "update.h"
 #include "modify.h"
@@ -43,10 +42,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
-#include "thermo.h"
-#include "output.h"
 #include "neighbor.h"
-#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -371,7 +367,7 @@ void FixGCMC::options(int narg, char **arg)
                            ngrouptypesmax*sizeof(char *),
                            "fix_gcmc:grouptypestrings");
       }
-      grouptypes[ngrouptypes] = atoi(arg[iarg+1]);
+      grouptypes[ngrouptypes] = force->inumeric(FLERR,arg[iarg+1]);
       int n = strlen(arg[iarg+2]) + 1;
       grouptypestrings[ngrouptypes] = new char[n];
       strcpy(grouptypestrings[ngrouptypes],arg[iarg+2]);
diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h
index 5d0b7aab8f..da4232d19b 100644
--- a/src/MC/fix_gcmc.h
+++ b/src/MC/fix_gcmc.h
@@ -20,7 +20,6 @@ FixStyle(gcmc,FixGCMC)
 #ifndef LMP_FIX_GCMC_H
 #define LMP_FIX_GCMC_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp
index 46c5e592ae..e57f1cdf4a 100644
--- a/src/MC/fix_tfmc.cpp
+++ b/src/MC/fix_tfmc.cpp
@@ -22,7 +22,6 @@
 #include <cfloat>
 #include "atom.h"
 #include "force.h"
-#include "update.h"
 #include "group.h"
 #include "random_mars.h"
 #include "comm.h"
diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp
index c71eaa2295..43bffa7e8d 100644
--- a/src/MC/pair_dsmc.cpp
+++ b/src/MC/pair_dsmc.cpp
@@ -15,12 +15,10 @@
    Contributing authors: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <climits>
 #include "pair_dsmc.h"
+#include <mpi.h>
+#include <cmath>
+#include <climits>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
index 727481dcc0..7d4ae13f0f 100644
--- a/src/MESSAGE/fix_client_md.cpp
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_client_md.h"
 #include <cstdio>
 #include <cstring>
-#include "fix_client_md.h"
 #include "update.h"
 #include "atom.h"
 #include "comm.h"
diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp
index 61221ca26e..f8fc349746 100644
--- a/src/MESSAGE/message.cpp
+++ b/src/MESSAGE/message.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "message.h"
+#include <cstring>
 #include "error.h"
 
 // CSlib interface
diff --git a/src/MESSAGE/server.cpp b/src/MESSAGE/server.cpp
index f587fb76df..dbcec08488 100644
--- a/src/MESSAGE/server.cpp
+++ b/src/MESSAGE/server.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "server.h"
+#include <cstring>
 #include "error.h"
 
 // customize by adding a new server protocol include and enum
diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp
index bef327616e..e16095ad4c 100644
--- a/src/MESSAGE/server_md.cpp
+++ b/src/MESSAGE/server_md.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "server_md.h"
 #include <mpi.h>
 #include <cstring>
-#include "server_md.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "update.h"
diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/MISC/compute_msd_nongauss.cpp
index f6291f4204..6123bf49af 100644
--- a/src/MISC/compute_msd_nongauss.cpp
+++ b/src/MISC/compute_msd_nongauss.cpp
@@ -15,14 +15,13 @@
    Contributing authors: Rob Hoy
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_msd_nongauss.h"
+#include <mpi.h>
 #include "atom.h"
 #include "update.h"
 #include "group.h"
 #include "domain.h"
 #include "fix_store.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp
index d2e43a9f69..06188de238 100644
--- a/src/MISC/compute_ti.cpp
+++ b/src/MISC/compute_ti.cpp
@@ -15,12 +15,11 @@
    Contributing author: Sai Jayaraman (University of Notre Dame)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include "atom.h"
-#include <cstring>
 #include "compute_ti.h"
+#include <mpi.h>
+#include <cstring>
+#include "atom.h"
 #include "update.h"
-#include "modify.h"
 #include "domain.h"
 #include "force.h"
 #include "pair.h"
diff --git a/src/MISC/dump_xtc.cpp b/src/MISC/dump_xtc.cpp
index a82cba20bd..1a2b71ab6d 100644
--- a/src/MISC/dump_xtc.cpp
+++ b/src/MISC/dump_xtc.cpp
@@ -22,12 +22,11 @@
                            support for groups
 ------------------------------------------------------------------------- */
 
+#include "dump_xtc.h"
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 #include <climits>
-#include "dump_xtc.h"
 #include "domain.h"
 #include "atom.h"
 #include "update.h"
diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp
index 66aed34846..c9d4958594 100644
--- a/src/MISC/fix_deposit.cpp
+++ b/src/MISC/fix_deposit.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_deposit.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h
index 38958b80e7..e3104c890d 100644
--- a/src/MISC/fix_deposit.h
+++ b/src/MISC/fix_deposit.h
@@ -20,7 +20,6 @@ FixStyle(deposit,FixDeposit)
 #ifndef LMP_FIX_DEPOSIT_H
 #define LMP_FIX_DEPOSIT_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp
index 004c8ad7bc..5a13b93b91 100644
--- a/src/MISC/fix_efield.cpp
+++ b/src/MISC/fix_efield.cpp
@@ -16,10 +16,9 @@
                         Stan Moore (Sandia) for dipole terms
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
 #include "fix_efield.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp
index 1bf7a15f1f..d868254c50 100644
--- a/src/MISC/fix_evaporate.cpp
+++ b/src/MISC/fix_evaporate.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_evaporate.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
@@ -25,7 +24,6 @@
 #include "force.h"
 #include "group.h"
 #include "random_park.h"
-#include "random_mars.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp
index 2bf02889a5..380c038e4a 100644
--- a/src/MISC/fix_gld.cpp
+++ b/src/MISC/fix_gld.cpp
@@ -16,18 +16,15 @@
                          Andrew Baczewski (Michigan State/SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_gld.h"
-#include "math_extra.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "respa.h"
 #include "comm.h"
-#include "input.h"
-#include "variable.h"
 #include "random_mars.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp
index 73853775a3..68a27b68be 100644
--- a/src/MISC/fix_oneway.cpp
+++ b/src/MISC/fix_oneway.cpp
@@ -15,14 +15,13 @@
    Contributing author: Axel Kohlmeyer (ICTP, Italy)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_oneway.h"
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "error.h"
 #include "force.h"
 #include "region.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp
index 02cce5a014..1453ceb317 100644
--- a/src/MISC/fix_orient_bcc.cpp
+++ b/src/MISC/fix_orient_bcc.cpp
@@ -18,11 +18,11 @@
             (https://dx.doi.org/10.6084/m9.figshare.1488628.v1
 ------------------------------------------------------------------------- */
 
+#include "fix_orient_bcc.h"
 #include <cmath>
 #include <cstring>
 #include <cstdlib>
 #include <mpi.h>
-#include "fix_orient_bcc.h"
 #include "atom.h"
 #include "update.h"
 #include "respa.h"
@@ -30,7 +30,6 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "comm.h"
-#include "output.h"
 #include "force.h"
 #include "math_const.h"
 #include "citeme.h"
diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp
index fc827ceb8f..082ecaf459 100644
--- a/src/MISC/fix_orient_fcc.cpp
+++ b/src/MISC/fix_orient_fcc.cpp
@@ -15,11 +15,11 @@
    Contributing authors: Koenraad Janssens and David Olmsted (SNL)
 ------------------------------------------------------------------------- */
 
+#include "fix_orient_fcc.h"
 #include <cmath>
 #include <cstring>
 #include <cstdlib>
 #include <mpi.h>
-#include "fix_orient_fcc.h"
 #include "atom.h"
 #include "update.h"
 #include "respa.h"
@@ -27,7 +27,6 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "comm.h"
-#include "output.h"
 #include "force.h"
 #include "math_const.h"
 #include "citeme.h"
diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/MISC/fix_thermal_conductivity.cpp
index f1aec3ff69..d0add6fecb 100644
--- a/src/MISC/fix_thermal_conductivity.cpp
+++ b/src/MISC/fix_thermal_conductivity.cpp
@@ -16,11 +16,9 @@
                         for swapping atoms of different masses
 ------------------------------------------------------------------------- */
 
-#include <cmath>
+#include "fix_thermal_conductivity.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdlib>
-#include "fix_thermal_conductivity.h"
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp
index 170103b0d0..eb9eb2620d 100644
--- a/src/MISC/fix_ttm.cpp
+++ b/src/MISC/fix_ttm.cpp
@@ -16,16 +16,14 @@
                          Carolyn Phillips (University of Michigan)
 ------------------------------------------------------------------------- */
 
+#include "fix_ttm.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_ttm.h"
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "domain.h"
-#include "region.h"
 #include "respa.h"
 #include "comm.h"
 #include "random_mars.h"
diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp
index 8e33c1c614..d5a97cd4b0 100644
--- a/src/MISC/fix_viscosity.cpp
+++ b/src/MISC/fix_viscosity.cpp
@@ -16,11 +16,10 @@
                         for swapping atoms of different masses
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <mpi.h>
-#include <cstring>
-#include <cstdlib>
 #include "fix_viscosity.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "modify.h"
diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp
index 124832b63e..a084491a78 100644
--- a/src/MISC/pair_nm_cut.cpp
+++ b/src/MISC/pair_nm_cut.cpp
@@ -15,11 +15,10 @@
    Contributing Author: Julien Devemy (ICCF)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_nm_cut.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp
index a8428ab980..df8a34062a 100644
--- a/src/MISC/pair_nm_cut_coul_cut.cpp
+++ b/src/MISC/pair_nm_cut_coul_cut.cpp
@@ -15,11 +15,10 @@
    Contributing Author: Julien Devemy (ICCF)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_nm_cut_coul_cut.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp
index af21f02881..4109fb0d9e 100644
--- a/src/MISC/pair_nm_cut_coul_long.cpp
+++ b/src/MISC/pair_nm_cut_coul_long.cpp
@@ -15,20 +15,16 @@
    Contributing Author: Julien Devemy (ICCF)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_nm_cut_coul_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
-#include "update.h"
-#include "integrate.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/MISC/xdr_compat.cpp b/src/MISC/xdr_compat.cpp
index 2d8d0ce7e5..9806b0bbd2 100644
--- a/src/MISC/xdr_compat.cpp
+++ b/src/MISC/xdr_compat.cpp
@@ -1,7 +1,6 @@
-#include <cstdlib>
-#include <climits>
-#include <cstring>
 #include "xdr_compat.h"
+#include <cstdlib>
+#include <cstring>
 
 /* This file is needed for systems, that do not provide XDR support
  * in their system libraries. It was written for windows, but will
diff --git a/src/MISC/xdr_compat.h b/src/MISC/xdr_compat.h
index 3062235080..5dfa01e0e8 100644
--- a/src/MISC/xdr_compat.h
+++ b/src/MISC/xdr_compat.h
@@ -3,7 +3,6 @@
 
 #include <climits>
 #include <cstdio>
-#include <cstdlib>
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp
index efd1c682f7..8a45f29368 100644
--- a/src/MOLECULE/angle_charmm.cpp
+++ b/src/MOLECULE/angle_charmm.cpp
@@ -15,9 +15,9 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_charmm.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/MOLECULE/angle_charmm.h b/src/MOLECULE/angle_charmm.h
index 2228ad8732..444c833d37 100644
--- a/src/MOLECULE/angle_charmm.h
+++ b/src/MOLECULE/angle_charmm.h
@@ -20,7 +20,6 @@ AngleStyle(charmm,AngleCharmm)
 #ifndef LMP_ANGLE_CHARMM_H
 #define LMP_ANGLE_CHARMM_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp
index 6e1b9fa2fb..645cf66ff2 100644
--- a/src/MOLECULE/angle_cosine.cpp
+++ b/src/MOLECULE/angle_cosine.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_cosine.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/MOLECULE/angle_cosine.h b/src/MOLECULE/angle_cosine.h
index f2406bc5dd..ca1f4178f8 100644
--- a/src/MOLECULE/angle_cosine.h
+++ b/src/MOLECULE/angle_cosine.h
@@ -20,7 +20,6 @@ AngleStyle(cosine,AngleCosine)
 #ifndef LMP_ANGLE_COSINE_H
 #define LMP_ANGLE_COSINE_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_cosine_delta.cpp b/src/MOLECULE/angle_cosine_delta.cpp
index eca10970f2..679a8deb0e 100644
--- a/src/MOLECULE/angle_cosine_delta.cpp
+++ b/src/MOLECULE/angle_cosine_delta.cpp
@@ -15,16 +15,12 @@
    Contributing author: Axel Kohlmeyer (Temple U), akohlmey at gmail.com
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_cosine_delta.h"
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
-#include "comm.h"
 #include "force.h"
-#include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/MOLECULE/angle_cosine_delta.h b/src/MOLECULE/angle_cosine_delta.h
index 1e19ecaf79..70b574b234 100644
--- a/src/MOLECULE/angle_cosine_delta.h
+++ b/src/MOLECULE/angle_cosine_delta.h
@@ -20,7 +20,6 @@ AngleStyle(cosine/delta,AngleCosineDelta)
 #ifndef LMP_ANGLE_COSINE_DELTA_H
 #define LMP_ANGLE_COSINE_DELTA_H
 
-#include <cstdio>
 #include "angle_cosine_squared.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp
index cb0a26871a..22c2f7ce8b 100644
--- a/src/MOLECULE/angle_cosine_periodic.cpp
+++ b/src/MOLECULE/angle_cosine_periodic.cpp
@@ -15,9 +15,9 @@
    Contributing author: Tod A Pascal (Caltech)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_cosine_periodic.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/MOLECULE/angle_cosine_periodic.h b/src/MOLECULE/angle_cosine_periodic.h
index e131e85101..f0188b6c17 100644
--- a/src/MOLECULE/angle_cosine_periodic.h
+++ b/src/MOLECULE/angle_cosine_periodic.h
@@ -20,7 +20,6 @@ AngleStyle(cosine/periodic, AngleCosinePeriodic)
 #ifndef LMP_ANGLE_PERIODIC_H
 #define LMP_ANGLE_PERIODIC_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp
index 28d63344a4..56b3ee58cf 100644
--- a/src/MOLECULE/angle_cosine_squared.cpp
+++ b/src/MOLECULE/angle_cosine_squared.cpp
@@ -15,9 +15,9 @@
    Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_cosine_squared.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/MOLECULE/angle_cosine_squared.h b/src/MOLECULE/angle_cosine_squared.h
index 8e8c84c0f9..a19a923850 100644
--- a/src/MOLECULE/angle_cosine_squared.h
+++ b/src/MOLECULE/angle_cosine_squared.h
@@ -20,7 +20,6 @@ AngleStyle(cosine/squared,AngleCosineSquared)
 #ifndef LMP_ANGLE_COSINE_SQUARED_H
 #define LMP_ANGLE_COSINE_SQUARED_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp
index 48b493d9b2..2e96884c9d 100644
--- a/src/MOLECULE/angle_harmonic.cpp
+++ b/src/MOLECULE/angle_harmonic.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_harmonic.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/MOLECULE/angle_harmonic.h b/src/MOLECULE/angle_harmonic.h
index e0c067653b..f371178d58 100644
--- a/src/MOLECULE/angle_harmonic.h
+++ b/src/MOLECULE/angle_harmonic.h
@@ -20,7 +20,6 @@ AngleStyle(harmonic,AngleHarmonic)
 #ifndef LMP_ANGLE_HARMONIC_H
 #define LMP_ANGLE_HARMONIC_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp
index 898ce49be7..54046c2ba8 100644
--- a/src/MOLECULE/angle_table.cpp
+++ b/src/MOLECULE/angle_table.cpp
@@ -15,10 +15,11 @@
    Contributing author: Chuanfu Luo (luochuanfu@gmail.com)
 ------------------------------------------------------------------------- */
 
+#include "angle_table.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "angle_table.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/MOLECULE/angle_table.h b/src/MOLECULE/angle_table.h
index 81e6c2ed89..8c854dc2e6 100644
--- a/src/MOLECULE/angle_table.h
+++ b/src/MOLECULE/angle_table.h
@@ -20,7 +20,6 @@ AngleStyle(table,AngleTable)
 #ifndef LMP_ANGLE_TABLE_H
 #define LMP_ANGLE_TABLE_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp
index bdafdae148..4eba471b8f 100644
--- a/src/MOLECULE/atom_vec_angle.cpp
+++ b/src/MOLECULE/atom_vec_angle.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_angle.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "memory.h"
diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp
index 275c424941..0bcd614f94 100644
--- a/src/MOLECULE/atom_vec_bond.cpp
+++ b/src/MOLECULE/atom_vec_bond.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_bond.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "memory.h"
diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp
index 036324cb2c..76c60ba121 100644
--- a/src/MOLECULE/atom_vec_full.cpp
+++ b/src/MOLECULE/atom_vec_full.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_full.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "memory.h"
diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp
index 49606f0a69..73cec70456 100644
--- a/src/MOLECULE/atom_vec_molecular.cpp
+++ b/src/MOLECULE/atom_vec_molecular.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_molecular.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "memory.h"
diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp
index 14e7736b50..c9ccfc6d2b 100644
--- a/src/MOLECULE/atom_vec_template.cpp
+++ b/src/MOLECULE/atom_vec_template.cpp
@@ -11,12 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "atom_vec_template.h"
 #include "atom.h"
 #include "molecule.h"
-#include "force.h"
 #include "comm.h"
 #include "domain.h"
 #include "modify.h"
diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp
index c023a7e81e..776291701b 100644
--- a/src/MOLECULE/bond_fene.cpp
+++ b/src/MOLECULE/bond_fene.cpp
@@ -11,12 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "bond_fene.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/MOLECULE/bond_fene.h b/src/MOLECULE/bond_fene.h
index 58cd6ce289..1963e3ca22 100644
--- a/src/MOLECULE/bond_fene.h
+++ b/src/MOLECULE/bond_fene.h
@@ -20,7 +20,6 @@ BondStyle(fene,BondFENE)
 #ifndef LMP_BOND_FENE_H
 #define LMP_BOND_FENE_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp
index b1bfdc6a1b..d03dfd9125 100644
--- a/src/MOLECULE/bond_fene_expand.cpp
+++ b/src/MOLECULE/bond_fene_expand.cpp
@@ -11,12 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "bond_fene_expand.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/MOLECULE/bond_fene_expand.h b/src/MOLECULE/bond_fene_expand.h
index cb316ac5f2..8cfc17dc68 100644
--- a/src/MOLECULE/bond_fene_expand.h
+++ b/src/MOLECULE/bond_fene_expand.h
@@ -20,7 +20,6 @@ BondStyle(fene/expand,BondFENEExpand)
 #ifndef LMP_BOND_FENE_EXPAND_H
 #define LMP_BOND_FENE_EXPAND_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp
index f65adeb2cb..284c9202fd 100644
--- a/src/MOLECULE/bond_gromos.cpp
+++ b/src/MOLECULE/bond_gromos.cpp
@@ -15,13 +15,11 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "bond_gromos.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/MOLECULE/bond_gromos.h b/src/MOLECULE/bond_gromos.h
index c26ad64b3d..966b914437 100644
--- a/src/MOLECULE/bond_gromos.h
+++ b/src/MOLECULE/bond_gromos.h
@@ -20,7 +20,6 @@ BondStyle(gromos,BondGromos)
 #ifndef LMP_BOND_GROMOS_H
 #define LMP_BOND_GROMOS_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp
index cb8434ce6e..7b19034629 100644
--- a/src/MOLECULE/bond_harmonic.cpp
+++ b/src/MOLECULE/bond_harmonic.cpp
@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "bond_harmonic.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/MOLECULE/bond_harmonic.h b/src/MOLECULE/bond_harmonic.h
index 5c692b2a8e..576e63629b 100644
--- a/src/MOLECULE/bond_harmonic.h
+++ b/src/MOLECULE/bond_harmonic.h
@@ -20,7 +20,6 @@ BondStyle(harmonic,BondHarmonic)
 #ifndef LMP_BOND_HARMONIC_H
 #define LMP_BOND_HARMONIC_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp
index 91dd2dbc49..6e16070cae 100644
--- a/src/MOLECULE/bond_morse.cpp
+++ b/src/MOLECULE/bond_morse.cpp
@@ -15,12 +15,11 @@
    Contributing author: Jeff Greathouse (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "bond_morse.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/MOLECULE/bond_morse.h b/src/MOLECULE/bond_morse.h
index c4d60bc217..030a94a8da 100644
--- a/src/MOLECULE/bond_morse.h
+++ b/src/MOLECULE/bond_morse.h
@@ -20,7 +20,6 @@ BondStyle(morse,BondMorse)
 #ifndef LMP_BOND_MORSE_H
 #define LMP_BOND_MORSE_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp
index 9999ead47f..e06b1b9aac 100644
--- a/src/MOLECULE/bond_nonlinear.cpp
+++ b/src/MOLECULE/bond_nonlinear.cpp
@@ -11,12 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "bond_nonlinear.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/MOLECULE/bond_nonlinear.h b/src/MOLECULE/bond_nonlinear.h
index 175421264b..7782b93778 100644
--- a/src/MOLECULE/bond_nonlinear.h
+++ b/src/MOLECULE/bond_nonlinear.h
@@ -20,7 +20,6 @@ BondStyle(nonlinear,BondNonlinear)
 #ifndef LMP_BOND_NONLINEAR_H
 #define LMP_BOND_NONLINEAR_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp
index 895202ff00..352b642bbe 100644
--- a/src/MOLECULE/bond_quartic.cpp
+++ b/src/MOLECULE/bond_quartic.cpp
@@ -15,14 +15,12 @@
    Contributing authors: Chris Lorenz and Mark Stevens (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "bond_quartic.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
-#include "update.h"
 #include "force.h"
 #include "pair.h"
 #include "memory.h"
diff --git a/src/MOLECULE/bond_quartic.h b/src/MOLECULE/bond_quartic.h
index 2aaa76e2c3..60ccf307b9 100644
--- a/src/MOLECULE/bond_quartic.h
+++ b/src/MOLECULE/bond_quartic.h
@@ -20,7 +20,6 @@ BondStyle(quartic,BondQuartic)
 #ifndef LMP_BOND_QUARTIC_H
 #define LMP_BOND_QUARTIC_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp
index 170afc27f0..ce41303a7d 100644
--- a/src/MOLECULE/bond_table.cpp
+++ b/src/MOLECULE/bond_table.cpp
@@ -15,13 +15,13 @@
    Contributing author: Chuanfu Luo (luochuanfu@gmail.com)
 ------------------------------------------------------------------------- */
 
+#include "bond_table.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "bond_table.h"
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/MOLECULE/bond_table.h b/src/MOLECULE/bond_table.h
index 5d4f2e8493..b08059415b 100644
--- a/src/MOLECULE/bond_table.h
+++ b/src/MOLECULE/bond_table.h
@@ -20,7 +20,6 @@ BondStyle(table,BondTable)
 #ifndef LMP_BOND_TABLE_H
 #define LMP_BOND_TABLE_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp
index 68c62eb4fd..8cc0713024 100644
--- a/src/MOLECULE/dihedral_charmm.cpp
+++ b/src/MOLECULE/dihedral_charmm.cpp
@@ -15,15 +15,13 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
+#include "dihedral_charmm.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "dihedral_charmm.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "pair.h"
 #include "update.h"
diff --git a/src/MOLECULE/dihedral_charmm.h b/src/MOLECULE/dihedral_charmm.h
index 8f51b398db..4be3925dad 100644
--- a/src/MOLECULE/dihedral_charmm.h
+++ b/src/MOLECULE/dihedral_charmm.h
@@ -20,7 +20,6 @@ DihedralStyle(charmm,DihedralCharmm)
 #ifndef LMP_DIHEDRAL_CHARMM_H
 #define LMP_DIHEDRAL_CHARMM_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp
index f65d01e9ed..f384c4cd36 100644
--- a/src/MOLECULE/dihedral_charmmfsw.cpp
+++ b/src/MOLECULE/dihedral_charmmfsw.cpp
@@ -18,15 +18,13 @@
      with additional assistance from Robert A. Latour, Clemson University
 ------------------------------------------------------------------------- */
 
+#include "dihedral_charmmfsw.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "dihedral_charmmfsw.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "pair.h"
 #include "update.h"
diff --git a/src/MOLECULE/dihedral_charmmfsw.h b/src/MOLECULE/dihedral_charmmfsw.h
index dd31067a8d..b33250004b 100644
--- a/src/MOLECULE/dihedral_charmmfsw.h
+++ b/src/MOLECULE/dihedral_charmmfsw.h
@@ -20,7 +20,6 @@ DihedralStyle(charmmfsw,DihedralCharmmfsw)
 #ifndef LMP_DIHEDRAL_CHARMMFSW_H
 #define LMP_DIHEDRAL_CHARMMFSW_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp
index ddb94dc571..f1e5811a84 100644
--- a/src/MOLECULE/dihedral_harmonic.cpp
+++ b/src/MOLECULE/dihedral_harmonic.cpp
@@ -15,14 +15,12 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
+#include "dihedral_harmonic.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "dihedral_harmonic.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "memory.h"
diff --git a/src/MOLECULE/dihedral_harmonic.h b/src/MOLECULE/dihedral_harmonic.h
index 2031261256..938e59918b 100644
--- a/src/MOLECULE/dihedral_harmonic.h
+++ b/src/MOLECULE/dihedral_harmonic.h
@@ -20,7 +20,6 @@ DihedralStyle(harmonic,DihedralHarmonic)
 #ifndef LMP_DIHEDRAL_HARMONIC_H
 #define LMP_DIHEDRAL_HARMONIC_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp
index d19731c097..56f7a3b5e8 100644
--- a/src/MOLECULE/dihedral_helix.cpp
+++ b/src/MOLECULE/dihedral_helix.cpp
@@ -16,13 +16,11 @@
                          Mark Stevens (Sandia)
 ------------------------------------------------------------------------- */
 
+#include "dihedral_helix.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "dihedral_helix.h"
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "update.h"
diff --git a/src/MOLECULE/dihedral_helix.h b/src/MOLECULE/dihedral_helix.h
index 745ab84115..0213c59e8a 100644
--- a/src/MOLECULE/dihedral_helix.h
+++ b/src/MOLECULE/dihedral_helix.h
@@ -20,7 +20,6 @@ DihedralStyle(helix,DihedralHelix)
 #ifndef LMP_DIHEDRAL_HELIX_H
 #define LMP_DIHEDRAL_HELIX_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp
index 04e7bbb627..eda7cede3e 100644
--- a/src/MOLECULE/dihedral_multi_harmonic.cpp
+++ b/src/MOLECULE/dihedral_multi_harmonic.cpp
@@ -15,12 +15,11 @@
    Contributing author: Mathias Puetz (SNL) and friends
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "dihedral_multi_harmonic.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "update.h"
diff --git a/src/MOLECULE/dihedral_multi_harmonic.h b/src/MOLECULE/dihedral_multi_harmonic.h
index 32f17e75ae..bb3d7183f7 100644
--- a/src/MOLECULE/dihedral_multi_harmonic.h
+++ b/src/MOLECULE/dihedral_multi_harmonic.h
@@ -20,7 +20,6 @@ DihedralStyle(multi/harmonic,DihedralMultiHarmonic)
 #ifndef LMP_DIHEDRAL_MULTI_HARMONIC_H
 #define LMP_DIHEDRAL_MULTI_HARMONIC_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp
index 293245e411..556efd850a 100644
--- a/src/MOLECULE/dihedral_opls.cpp
+++ b/src/MOLECULE/dihedral_opls.cpp
@@ -15,13 +15,12 @@
    Contributing author: Mark Stevens (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "dihedral_opls.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "memory.h"
diff --git a/src/MOLECULE/dihedral_opls.h b/src/MOLECULE/dihedral_opls.h
index c1e64ada1e..01878173cd 100644
--- a/src/MOLECULE/dihedral_opls.h
+++ b/src/MOLECULE/dihedral_opls.h
@@ -20,7 +20,6 @@ DihedralStyle(opls,DihedralOPLS)
 #ifndef LMP_DIHEDRAL_OPLS_H
 #define LMP_DIHEDRAL_OPLS_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp
index 3395c7ef14..fb0a550898 100644
--- a/src/MOLECULE/fix_cmap.cpp
+++ b/src/MOLECULE/fix_cmap.cpp
@@ -27,20 +27,16 @@
    - MacKerell et al., J. Comput. Chem. 25(2004):1400-1415.
 ------------------------------------------------------------------------- */
 
+#include "fix_cmap.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include <cstdio>
-#include "fix_cmap.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "update.h"
 #include "respa.h"
-#include "modify.h"
 #include "domain.h"
 #include "force.h"
-#include "group.h"
 #include "comm.h"
 #include "math_const.h"
 #include "memory.h"
diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp
index 01e9729e80..abd2d4e11e 100644
--- a/src/MOLECULE/improper_cvff.cpp
+++ b/src/MOLECULE/improper_cvff.cpp
@@ -11,14 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "improper_cvff.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "improper_cvff.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "memory.h"
diff --git a/src/MOLECULE/improper_cvff.h b/src/MOLECULE/improper_cvff.h
index d4c30cc2ee..055d2ca9b8 100644
--- a/src/MOLECULE/improper_cvff.h
+++ b/src/MOLECULE/improper_cvff.h
@@ -20,7 +20,6 @@ ImproperStyle(cvff,ImproperCvff)
 #ifndef LMP_IMPROPER_CVFF_H
 #define LMP_IMPROPER_CVFF_H
 
-#include <cstdio>
 #include "improper.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp
index c5421fffdb..778fe646e1 100644
--- a/src/MOLECULE/improper_harmonic.cpp
+++ b/src/MOLECULE/improper_harmonic.cpp
@@ -11,14 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "improper_harmonic.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "improper_harmonic.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "math_const.h"
diff --git a/src/MOLECULE/improper_harmonic.h b/src/MOLECULE/improper_harmonic.h
index fbbb8d33d6..5949c6911e 100644
--- a/src/MOLECULE/improper_harmonic.h
+++ b/src/MOLECULE/improper_harmonic.h
@@ -20,7 +20,6 @@ ImproperStyle(harmonic,ImproperHarmonic)
 #ifndef LMP_IMPROPER_HARMONIC_H
 #define LMP_IMPROPER_HARMONIC_H
 
-#include <cstdio>
 #include "improper.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp
index 3de46df0f3..d3adf19993 100644
--- a/src/MOLECULE/improper_umbrella.cpp
+++ b/src/MOLECULE/improper_umbrella.cpp
@@ -15,14 +15,12 @@
    Contributing author: Tod A Pascal (Caltech)
 ------------------------------------------------------------------------- */
 
+#include "improper_umbrella.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "improper_umbrella.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "math_const.h"
diff --git a/src/MOLECULE/improper_umbrella.h b/src/MOLECULE/improper_umbrella.h
index dc2262d01c..da9d6c8f4b 100644
--- a/src/MOLECULE/improper_umbrella.h
+++ b/src/MOLECULE/improper_umbrella.h
@@ -20,7 +20,6 @@ ImproperStyle(umbrella,ImproperUmbrella)
 #ifndef LMP_IMPROPER_UMBRELLA_H
 #define LMP_IMPROPER_UMBRELLA_H
 
-#include <cstdio>
 #include "improper.h"
 
 namespace LAMMPS_NS {
diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
index ddc1110081..53c3101708 100644
--- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
@@ -15,15 +15,12 @@
    Contributing author: Tod A Pascal (Caltech)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_hbond_dreiding_lj.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_request.h"
diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
index 055f0ed46b..3039a662e6 100644
--- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
@@ -15,15 +15,12 @@
    Contributing author: Tod A Pascal (Caltech)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_hbond_dreiding_morse.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_request.h"
diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
index af4611e014..5ebfe0a110 100644
--- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
+++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
@@ -15,11 +15,10 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_charmm_coul_charmm.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
index d68d5e8f6d..ff7dbb290b 100644
--- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
+++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
@@ -11,8 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
 #include "pair_lj_charmm_coul_charmm_implicit.h"
 #include "atom.h"
 #include "force.h"
diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
index 0e1cbd85a5..4fb7cc5229 100644
--- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
+++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
@@ -19,11 +19,10 @@
      with additional assistance from Robert A. Latour, Clemson University
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_charmmfsw_coul_charmmfsh.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "comm.h"
diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
index 2b3d2c60f5..e5f25a511b 100644
--- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
+++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
@@ -15,10 +15,10 @@
    Contributing author: Pavel Elkind (Gothenburg University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_tip4p_cut.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "neighbor.h"
diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp
index e6fb9aab99..3a6702c9b2 100644
--- a/src/MOLECULE/pair_tip4p_cut.cpp
+++ b/src/MOLECULE/pair_tip4p_cut.cpp
@@ -15,9 +15,9 @@
    Contributing author: Pavel Elkind (Gothenburg University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_tip4p_cut.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "neighbor.h"
@@ -26,12 +26,10 @@
 #include "angle.h"
 #include "bond.h"
 #include "comm.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp
index f2f2991442..2b663554cc 100644
--- a/src/MPIIO/dump_atom_mpiio.cpp
+++ b/src/MPIIO/dump_atom_mpiio.cpp
@@ -15,12 +15,12 @@
    Contributing author: Paul Coffman (IBM)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "dump_atom_mpiio.h"
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
 #include "domain.h"
-#include "atom.h"
 #include "update.h"
-#include "group.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/MPIIO/dump_atom_mpiio.h b/src/MPIIO/dump_atom_mpiio.h
index ad49fa1182..36b43e3f08 100644
--- a/src/MPIIO/dump_atom_mpiio.h
+++ b/src/MPIIO/dump_atom_mpiio.h
@@ -21,7 +21,6 @@ DumpStyle(atom/mpiio,DumpAtomMPIIO)
 #define LMP_DUMP_ATOM_MPIIO_H
 
 #include "dump_atom.h"
-#include <cstdlib>
 
 namespace LAMMPS_NS {
 
diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp
index c580d2e7af..31848b550c 100644
--- a/src/MPIIO/dump_cfg_mpiio.cpp
+++ b/src/MPIIO/dump_cfg_mpiio.cpp
@@ -15,18 +15,12 @@
    Contributing author: Paul Coffman (IBM)
 ------------------------------------------------------------------------- */
 
+#include "dump_cfg_mpiio.h"
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "dump_cfg_mpiio.h"
 #include "atom.h"
 #include "domain.h"
-#include "comm.h"
-#include "modify.h"
-#include "compute.h"
-#include "input.h"
-#include "fix.h"
-#include "variable.h"
 #include "update.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp
index 3650ca994e..dca5833c5b 100644
--- a/src/MPIIO/dump_custom_mpiio.cpp
+++ b/src/MPIIO/dump_custom_mpiio.cpp
@@ -15,20 +15,15 @@
    Contributing author: Paul Coffman (IBM)
 ------------------------------------------------------------------------- */
 
+#include "dump_custom_mpiio.h"
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "dump_custom_mpiio.h"
-#include "atom.h"
-#include "force.h"
 #include "domain.h"
-#include "region.h"
-#include "group.h"
 #include "input.h"
 #include "variable.h"
 #include "update.h"
 #include "modify.h"
-#include "compute.h"
 #include "fix.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp
index f15d340cd1..f5caab3a9c 100644
--- a/src/MPIIO/dump_xyz_mpiio.cpp
+++ b/src/MPIIO/dump_xyz_mpiio.cpp
@@ -15,21 +15,13 @@
    Contributing author: Paul Coffman (IBM)
 ------------------------------------------------------------------------- */
 
+#include "dump_xyz_mpiio.h"
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "dump_xyz_mpiio.h"
-#include "atom.h"
-#include "force.h"
 #include "domain.h"
-#include "region.h"
-#include "group.h"
-#include "input.h"
-#include "variable.h"
 #include "update.h"
-#include "modify.h"
 #include "compute.h"
-#include "fix.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/MPIIO/restart_mpiio.cpp b/src/MPIIO/restart_mpiio.cpp
index 804df211dc..e8ef5c6c4e 100644
--- a/src/MPIIO/restart_mpiio.cpp
+++ b/src/MPIIO/restart_mpiio.cpp
@@ -15,9 +15,9 @@
    Contributing author: Paul Coffman (IBM)
 ------------------------------------------------------------------------- */
 
+#include "restart_mpiio.h"
 #include <mpi.h>
 #include <climits>
-#include "restart_mpiio.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/MSCG/fix_mscg.cpp b/src/MSCG/fix_mscg.cpp
index b282595240..caa9a528a7 100644
--- a/src/MSCG/fix_mscg.cpp
+++ b/src/MSCG/fix_mscg.cpp
@@ -15,10 +15,10 @@
    Contributing authors: Lauren Abbott (Sandia)
 ------------------------------------------------------------------------- */
 
+#include "fix_mscg.h"
 #include <mpi.h>
 #include <cstring>
 #include <cstdlib>
-#include "fix_mscg.h"
 #include "mscg.h"
 #include "atom.h"
 #include "comm.h"
diff --git a/src/Makefile b/src/Makefile
index d611adc404..5db09db65a 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -198,8 +198,8 @@ gitversion:
 # shlib = shared lib in Obj_shared_machine
 
 .DEFAULT:
-	@if [ $@ = "serial" -a ! -f STUBS/libmpi_stubs.a ]; \
-	  then $(MAKE) mpi-stubs; fi
+	@if [ $@ = "serial" ]; \
+	  then cd STUBS; $(MAKE); cd ..; fi
 	@test -f MAKE/Makefile.$@ -o -f MAKE/OPTIONS/Makefile.$@ -o \
 	  -f MAKE/MACHINES/Makefile.$@ -o -f MAKE/MINE/Makefile.$@
 	@if [ ! -d $(objdir) ]; then mkdir $(objdir); fi
@@ -256,7 +256,10 @@ clean:
 
 clean-all:
 	rm -rf Obj_*
+
 clean-%:
+	@if [ $@ = "clean-serial" ]; \
+		then cd STUBS; $(MAKE) clean; cd ..; fi
 	rm -rf Obj_$(@:clean-%=%) Obj_shared_$(@:clean-%=%)
 
 # Create Makefile.list
diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp
index fc2b6731ee..ad24aaee63 100644
--- a/src/OPT/pair_eam_opt.cpp
+++ b/src/OPT/pair_eam_opt.cpp
@@ -19,9 +19,9 @@
      Vincent Natoli, Stone Ridge Technology
 ------------------------------------------------------------------------- */
 
+#include "pair_eam_opt.h"
 #include <cmath>
 #include <cstdlib>
-#include "pair_eam_opt.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp
index d80d3d1ec4..3dc6bdb6b4 100644
--- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp
+++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp
@@ -18,9 +18,9 @@
      Vincent Natoli, Stone Ridge Technology
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_charmm_coul_long_opt.h"
 #include <cmath>
 #include <cstdlib>
-#include "pair_lj_charmm_coul_long_opt.h"
 #include "atom.h"
 #include "force.h"
 #include "neigh_list.h"
diff --git a/src/OPT/pair_lj_cut_coul_long_opt.cpp b/src/OPT/pair_lj_cut_coul_long_opt.cpp
index a25010cf1f..a1f97aaae9 100644
--- a/src/OPT/pair_lj_cut_coul_long_opt.cpp
+++ b/src/OPT/pair_lj_cut_coul_long_opt.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_lj_cut_coul_long_opt.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "neigh_list.h"
diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp
index c6684461be..3b3a19a9e8 100644
--- a/src/OPT/pair_lj_cut_opt.cpp
+++ b/src/OPT/pair_lj_cut_opt.cpp
@@ -18,8 +18,8 @@
      Vincent Natoli, Stone Ridge Technology
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "pair_lj_cut_opt.h"
+#include <cstdlib>
 #include "atom.h"
 #include "force.h"
 #include "neigh_list.h"
diff --git a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp
index 92facca43e..f8181d69a6 100644
--- a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp
+++ b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp
@@ -15,8 +15,8 @@
    OPT version: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_lj_cut_tip4p_long_opt.h"
+#include <cmath>
 #include "atom.h"
 #include "domain.h"
 #include "force.h"
diff --git a/src/OPT/pair_lj_long_coul_long_opt.cpp b/src/OPT/pair_lj_long_coul_long_opt.cpp
index 243b64391f..c323d078c4 100644
--- a/src/OPT/pair_lj_long_coul_long_opt.cpp
+++ b/src/OPT/pair_lj_long_coul_long_opt.cpp
@@ -15,8 +15,9 @@
    OPT version: Wayne Mitchell (Loyola University New Orleans)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_lj_long_coul_long_opt.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "neigh_list.h"
diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp
index c9c6bba355..1d2e226777 100644
--- a/src/OPT/pair_morse_opt.cpp
+++ b/src/OPT/pair_morse_opt.cpp
@@ -18,9 +18,9 @@
      Vincent Natoli, Stone Ridge Technology
 ------------------------------------------------------------------------- */
 
+#include "pair_morse_opt.h"
 #include <cmath>
 #include <cstdlib>
-#include "pair_morse_opt.h"
 #include "atom.h"
 #include "force.h"
 #include "neigh_list.h"
diff --git a/src/OPT/pair_ufm_opt.cpp b/src/OPT/pair_ufm_opt.cpp
index f463dac3f1..eabb093b18 100644
--- a/src/OPT/pair_ufm_opt.cpp
+++ b/src/OPT/pair_ufm_opt.cpp
@@ -17,9 +17,9 @@
             Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
  ------------------------------------------------------------------------- */
 
+#include "pair_ufm_opt.h"
 #include <cstdlib>
 #include <cmath>
-#include "pair_ufm_opt.h"
 #include "atom.h"
 #include "force.h"
 #include "neigh_list.h"
diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp
index c4fa0bd43b..3e3312bf01 100644
--- a/src/PERI/atom_vec_peri.cpp
+++ b/src/PERI/atom_vec_peri.cpp
@@ -15,14 +15,12 @@
    Contributing author: Mike Parks (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cfloat>
-#include <cstdlib>
-#include <cstring>
 #include "atom_vec_peri.h"
+#include <cfloat>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "citeme.h"
diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp
index 4bf8fa17a5..230b766725 100644
--- a/src/PERI/compute_damage_atom.cpp
+++ b/src/PERI/compute_damage_atom.cpp
@@ -15,14 +15,12 @@
    Contributing author: Mike Parks (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_damage_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
-#include "pair_peri_pmb.h"
 #include "fix_peri_neigh.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/PERI/compute_dilatation_atom.cpp b/src/PERI/compute_dilatation_atom.cpp
index 990731a227..095f619838 100644
--- a/src/PERI/compute_dilatation_atom.cpp
+++ b/src/PERI/compute_dilatation_atom.cpp
@@ -15,19 +15,17 @@
    Contributing author: Rezwanur Rahman, John Foster (UTSA)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_dilatation_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
+#include "fix.h"
 #include "force.h"
-#include "pair.h"
 #include "pair_peri_lps.h"
-#include "pair_peri_pmb.h"
 #include "pair_peri_ves.h"
 #include "pair_peri_eps.h"
-#include "fix_peri_neigh.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/PERI/compute_plasticity_atom.cpp b/src/PERI/compute_plasticity_atom.cpp
index d08fb98e07..e312630b62 100644
--- a/src/PERI/compute_plasticity_atom.cpp
+++ b/src/PERI/compute_plasticity_atom.cpp
@@ -15,15 +15,14 @@
    Contributing author: Rezwanur Rahman, John Foster (UTSA)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_plasticity_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
-#include "pair_peri_pmb.h"
 #include "fix_peri_neigh.h"
+#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp
index 66137e6a01..70f46dcdc1 100644
--- a/src/PERI/fix_peri_neigh.cpp
+++ b/src/PERI/fix_peri_neigh.cpp
@@ -15,9 +15,9 @@
    Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "fix_peri_neigh.h"
-#include "pair_peri_pmb.h"
+#include <mpi.h>
+#include <cmath>
 #include "pair_peri_lps.h"
 #include "pair_peri_ves.h"
 #include "pair_peri_eps.h"
@@ -25,7 +25,6 @@
 #include "domain.h"
 #include "force.h"
 #include "comm.h"
-#include "update.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp
index c00495ba4d..2579a9b75a 100644
--- a/src/PERI/pair_peri_eps.cpp
+++ b/src/PERI/pair_peri_eps.cpp
@@ -15,15 +15,14 @@
    Contributing author: Rezwanur Rahman, John Foster (UTSA)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "pair_peri_eps.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "lattice.h"
 #include "force.h"
-#include "update.h"
 #include "modify.h"
 #include "fix.h"
 #include "fix_peri_neigh.h"
@@ -32,7 +31,6 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
-#include "update.h"
 
 using namespace LAMMPS_NS;
 
@@ -451,12 +449,12 @@ void PairPeriEPS::coeff(int narg, char **arg)
   force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
   force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
 
-  double bulkmodulus_one = atof(arg[2]);
-  double shearmodulus_one = atof(arg[3]);
-  double cut_one = atof(arg[4]);
-  double s00_one = atof(arg[5]);
-  double alpha_one = atof(arg[6]);
-  double myieldstress_one = atof(arg[7]);
+  double bulkmodulus_one = force->numeric(FLERR,arg[2]);
+  double shearmodulus_one = force->numeric(FLERR,arg[3]);
+  double cut_one = force->numeric(FLERR,arg[4]);
+  double s00_one = force->numeric(FLERR,arg[5]);
+  double alpha_one = force->numeric(FLERR,arg[6]);
+  double myieldstress_one = force->numeric(FLERR,arg[7]);
 
   int count = 0;
   for (int i = ilo; i <= ihi; i++) {
diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp
index f0418c8c8d..f32ce5fb1c 100644
--- a/src/PERI/pair_peri_lps.cpp
+++ b/src/PERI/pair_peri_lps.cpp
@@ -15,15 +15,14 @@
    Contributing author: Mike Parks (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "pair_peri_lps.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "lattice.h"
 #include "force.h"
-#include "update.h"
 #include "modify.h"
 #include "fix.h"
 #include "fix_peri_neigh.h"
@@ -32,7 +31,6 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
-#include "update.h"
 #include "math_const.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp
index ad2f3fb7c7..ceab40d88d 100644
--- a/src/PERI/pair_peri_pmb.cpp
+++ b/src/PERI/pair_peri_pmb.cpp
@@ -15,23 +15,21 @@
    Contributing author: Mike Parks (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_peri_pmb.h"
+#include <mpi.h>
 #include <cmath>
 #include <cfloat>
-#include <cstdlib>
 #include <cstring>
-#include "pair_peri_pmb.h"
 #include "atom.h"
 #include "domain.h"
 #include "lattice.h"
 #include "force.h"
-#include "update.h"
 #include "modify.h"
 #include "fix.h"
 #include "fix_peri_neigh.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp
index 24a9f92a97..bd1eaa5fd2 100644
--- a/src/PERI/pair_peri_ves.cpp
+++ b/src/PERI/pair_peri_ves.cpp
@@ -15,15 +15,14 @@
    Contributing authors: Rezwanur Rahman, J.T. Foster (UTSA)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "pair_peri_ves.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "lattice.h"
 #include "force.h"
-#include "update.h"
 #include "modify.h"
 #include "fix.h"
 #include "fix_peri_neigh.h"
@@ -428,13 +427,13 @@ void PairPeriVES::coeff(int narg, char **arg)
   force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
   force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
 
-  double bulkmodulus_one = atof(arg[2]);
-  double shearmodulus_one = atof(arg[3]);
-  double cut_one = atof(arg[4]);
-  double s00_one = atof(arg[5]);
-  double alpha_one = atof(arg[6]);
-  double mlambdai_one = atof(arg[7]);
-  double mtaui_one = atof(arg[8]);
+  double bulkmodulus_one = force->numeric(FLERR,arg[2]);
+  double shearmodulus_one = force->numeric(FLERR,arg[3]);
+  double cut_one = force->numeric(FLERR,arg[4]);
+  double s00_one = force->numeric(FLERR,arg[5]);
+  double alpha_one = force->numeric(FLERR,arg[6]);
+  double mlambdai_one = force->numeric(FLERR,arg[7]);
+  double mtaui_one = force->numeric(FLERR,arg[8]);
 
   int count = 0;
   for (int i = ilo; i <= ihi; i++) {
diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp
index 41cfcede34..c8646f5b14 100644
--- a/src/POEMS/fix_poems.cpp
+++ b/src/POEMS/fix_poems.cpp
@@ -17,20 +17,18 @@
                   Kurt Anderson (anderk5@rpi.edu)
 ------------------------------------------------------------------------- */
 
+#include "fix_poems.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstring>
 #include <cstdlib>
 #include "workspace.h"
-#include "fix_poems.h"
 #include "atom.h"
 #include "domain.h"
 #include "update.h"
 #include "respa.h"
 #include "modify.h"
 #include "force.h"
-#include "output.h"
 #include "group.h"
 #include "comm.h"
 #include "citeme.h"
diff --git a/src/POEMS/fix_poems.h b/src/POEMS/fix_poems.h
index 7b2c77a1bd..6892c51d7e 100644
--- a/src/POEMS/fix_poems.h
+++ b/src/POEMS/fix_poems.h
@@ -22,6 +22,8 @@ FixStyle(poems,FixPOEMS)
 
 #include "fix.h"
 
+class Workspace;
+
 namespace LAMMPS_NS {
 
 class FixPOEMS : public Fix  {
@@ -94,7 +96,7 @@ class FixPOEMS : public Fix  {
 
   // POEMS object
 
-  class Workspace *poems;
+  Workspace *poems;
 
   // internal class functions
 
diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp
index 280c2d91e2..57ea2e9148 100644
--- a/src/PYTHON/fix_python_invoke.cpp
+++ b/src/PYTHON/fix_python_invoke.cpp
@@ -15,14 +15,11 @@
    Contributing author: Richard Berger (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <Python.h>
-#include <cstdio>
-#include <cstring>
 #include "fix_python_invoke.h"
-#include "atom.h"
+#include <Python.h>   // IWYU pragma: keep
+#include <cstring>
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
 #include "lmppython.h"
 #include "python_compat.h"
diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp
index ec21dbeadd..be63b851a2 100644
--- a/src/PYTHON/fix_python_move.cpp
+++ b/src/PYTHON/fix_python_move.cpp
@@ -15,16 +15,9 @@
    Contributing author: Richard Berger (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <Python.h>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "fix_python_move.h"
-#include "atom.h"
-#include "comm.h"
-#include "force.h"
-#include "memory.h"
-#include "neigh_list.h"
+#include <Python.h>   // IWYU pragma: keep
+#include <cstring>
 #include "lmppython.h"
 #include "error.h"
 #include "python_compat.h"
diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp
index 2148fc67b8..0d79a31946 100644
--- a/src/PYTHON/pair_python.cpp
+++ b/src/PYTHON/pair_python.cpp
@@ -15,13 +15,11 @@
    Contributing authors: Axel Kohlmeyer and Richard Berger (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <Python.h>
-#include <cstdio>
+#include "pair_python.h"
+#include <Python.h>  // IWYU pragma: keep
 #include <cstdlib>
 #include <cstring>
-#include "pair_python.h"
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
 #include "memory.h"
 #include "update.h"
diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp
index aaa4f74c69..1188942e75 100644
--- a/src/PYTHON/python_impl.cpp
+++ b/src/PYTHON/python_impl.cpp
@@ -15,8 +15,10 @@
    Contributing author: Richard Berger and Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <Python.h>
-#include "lmppython.h"
+#include "python_impl.h"
+#include <cstdlib>
+#include <cstring>
+#include <Python.h>  // IWYU pragma: keep
 #include "force.h"
 #include "input.h"
 #include "variable.h"
diff --git a/src/PYTHON/python_impl.h b/src/PYTHON/python_impl.h
index 2ccdda95c9..f890f54f3b 100644
--- a/src/PYTHON/python_impl.h
+++ b/src/PYTHON/python_impl.h
@@ -15,6 +15,7 @@
 #define LMP_PYTHON_IMPL_H
 
 #include "pointers.h"
+#include "lmppython.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp
index 0ab010b7bb..7768c01a41 100644
--- a/src/QEQ/fix_qeq.cpp
+++ b/src/QEQ/fix_qeq.cpp
@@ -16,29 +16,19 @@
      Based on fix qeq/reax by H. Metin Aktulga
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "fix_qeq.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "domain.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "update.h"
 #include "force.h"
-#include "kspace.h"
-#include "group.h"
-#include "pair.h"
-#include "respa.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace FixConst;
 
 #define MAXLINE 1024
diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp
index ba88f4f1c3..a2cc683b56 100644
--- a/src/QEQ/fix_qeq_dynamic.cpp
+++ b/src/QEQ/fix_qeq_dynamic.cpp
@@ -15,24 +15,21 @@
    Contributing author: Ray Shan (Sandia)
 ------------------------------------------------------------------------- */
 
+#include "fix_qeq_dynamic.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "fix_qeq_dynamic.h"
 #include "atom.h"
 #include "comm.h"
-#include "domain.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
 #include "force.h"
 #include "group.h"
-#include "pair.h"
 #include "kspace.h"
 #include "respa.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp
index 1e3686f99c..265528a089 100644
--- a/src/QEQ/fix_qeq_fire.cpp
+++ b/src/QEQ/fix_qeq_fire.cpp
@@ -15,26 +15,23 @@
    Contributing author: Ray Shan (Sandia)
 ------------------------------------------------------------------------- */
 
+#include "fix_qeq_fire.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "fix_qeq_fire.h"
 #include "atom.h"
 #include "comm.h"
-#include "domain.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
 #include "force.h"
 #include "group.h"
-#include "pair.h"
 #include "pair_comb.h"
 #include "pair_comb3.h"
 #include "kspace.h"
 #include "respa.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp
index 9517343974..8fb9fd3273 100644
--- a/src/QEQ/fix_qeq_point.cpp
+++ b/src/QEQ/fix_qeq_point.cpp
@@ -15,14 +15,11 @@
    Contributing author: Ray Shan (Sandia)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "fix_qeq_point.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "domain.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp
index 6367feacc5..37951adb1a 100644
--- a/src/QEQ/fix_qeq_shielded.cpp
+++ b/src/QEQ/fix_qeq_shielded.cpp
@@ -15,14 +15,11 @@
    Contributing author: Ray Shan (Sandia)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "fix_qeq_shielded.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "domain.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp
index 3443a519a2..4f5369eb87 100644
--- a/src/QEQ/fix_qeq_slater.cpp
+++ b/src/QEQ/fix_qeq_slater.cpp
@@ -15,14 +15,12 @@
    Contributing author: Ray Shan (Sandia)
 ------------------------------------------------------------------------- */
 
+#include "fix_qeq_slater.h"
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "fix_qeq_slater.h"
 #include "atom.h"
 #include "comm.h"
-#include "domain.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
@@ -33,7 +31,6 @@
 #include "kspace.h"
 #include "respa.h"
 #include "math_const.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp
index df14221586..a6abcce85d 100644
--- a/src/REPLICA/compute_event_displace.cpp
+++ b/src/REPLICA/compute_event_displace.cpp
@@ -15,16 +15,13 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "compute_event_displace.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "modify.h"
 #include "fix_event.h"
-#include "memory.h"
 #include "error.h"
 #include "force.h"
 #include "update.h"
diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp
index 8fc5de6b16..41f91332cb 100644
--- a/src/REPLICA/fix_event.cpp
+++ b/src/REPLICA/fix_event.cpp
@@ -15,17 +15,11 @@
    Contributing author: Mike Brown (SNL), Aidan Thompson (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_event.h"
 #include "atom.h"
-#include "update.h"
 #include "domain.h"
-#include "neighbor.h"
-#include "comm.h"
-#include "universe.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/REPLICA/fix_event_hyper.cpp b/src/REPLICA/fix_event_hyper.cpp
index eae1ad021d..0d32516dee 100644
--- a/src/REPLICA/fix_event_hyper.cpp
+++ b/src/REPLICA/fix_event_hyper.cpp
@@ -11,17 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_event_hyper.h"
-#include "atom.h"
-#include "update.h"
-#include "domain.h"
-#include "neighbor.h"
 #include "comm.h"
-#include "universe.h"
-#include "memory.h"
 #include "error.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/REPLICA/fix_event_prd.cpp b/src/REPLICA/fix_event_prd.cpp
index a311a6444a..19a89e988c 100644
--- a/src/REPLICA/fix_event_prd.cpp
+++ b/src/REPLICA/fix_event_prd.cpp
@@ -15,17 +15,10 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_event_prd.h"
-#include "atom.h"
-#include "update.h"
-#include "domain.h"
-#include "neighbor.h"
 #include "comm.h"
-#include "universe.h"
-#include "memory.h"
 #include "error.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/REPLICA/fix_event_tad.cpp b/src/REPLICA/fix_event_tad.cpp
index 0916fdf493..d0b94a216b 100644
--- a/src/REPLICA/fix_event_tad.cpp
+++ b/src/REPLICA/fix_event_tad.cpp
@@ -15,17 +15,10 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_event_tad.h"
-#include "atom.h"
-#include "update.h"
-#include "domain.h"
-#include "neighbor.h"
 #include "comm.h"
-#include "universe.h"
-#include "memory.h"
 #include "error.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/REPLICA/fix_hyper.cpp b/src/REPLICA/fix_hyper.cpp
index c86c00ad45..21a4fde04d 100644
--- a/src/REPLICA/fix_hyper.cpp
+++ b/src/REPLICA/fix_hyper.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_hyper.h"
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp
index 0c76b29911..5e9da02768 100644
--- a/src/REPLICA/fix_hyper_global.cpp
+++ b/src/REPLICA/fix_hyper_global.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_hyper_global.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstring>
-#include "fix_hyper_global.h"
 #include "atom.h"
 #include "update.h"
 #include "force.h"
@@ -24,7 +23,6 @@
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "neigh_list.h"
-#include "modify.h"
 #include "math_extra.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp
index a6db4419f0..e8773095d1 100644
--- a/src/REPLICA/fix_hyper_local.cpp
+++ b/src/REPLICA/fix_hyper_local.cpp
@@ -11,21 +11,20 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_hyper_local.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstring>
-#include "fix_hyper_local.h"
 #include "atom.h"
 #include "update.h"
 #include "force.h"
 #include "pair.h"
 #include "domain.h"
 #include "comm.h"
+#include "my_page.h"
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "neigh_list.h"
-#include "modify.h"
 #include "math_extra.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/REPLICA/fix_hyper_local.h b/src/REPLICA/fix_hyper_local.h
index 6f13acb606..8fb3a445c2 100644
--- a/src/REPLICA/fix_hyper_local.h
+++ b/src/REPLICA/fix_hyper_local.h
@@ -21,7 +21,6 @@ FixStyle(hyper/local,FixHyperLocal)
 #define LMP_FIX_HYPER_LOCAL_H
 
 #include "fix_hyper.h"
-#include "my_page.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp
index e1b1e46a53..7b377ae9ec 100644
--- a/src/REPLICA/fix_neb.cpp
+++ b/src/REPLICA/fix_neb.cpp
@@ -16,11 +16,10 @@
      new options for inter-replica forces, first/last replica treatment
 ------------------------------------------------------------------------- */
 
+#include "fix_neb.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "fix_neb.h"
 #include "universe.h"
 #include "update.h"
 #include "atom.h"
diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp
index 00b91684e9..af2a963616 100644
--- a/src/REPLICA/hyper.cpp
+++ b/src/REPLICA/hyper.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "hyper.h"
+#include <mpi.h>
+#include <cstring>
 #include "update.h"
-#include "atom.h"
 #include "domain.h"
 #include "region.h"
 #include "integrate.h"
diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp
index 4061ec6541..dafc0c0875 100644
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@@ -11,16 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h
-// due to OpenMPI bug which sets INT64_MAX via its mpi.h
-//   before lmptype.h can set flags to insure it is done correctly
-
-#include "lmptype.h"
+#include "neb.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "neb.h"
 #include "universe.h"
 #include "atom.h"
 #include "update.h"
diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h
index f585a0c8a7..b53992711c 100644
--- a/src/REPLICA/neb.h
+++ b/src/REPLICA/neb.h
@@ -20,7 +20,6 @@ CommandStyle(neb,NEB)
 #ifndef LMP_NEB_H
 #define LMP_NEB_H
 
-#include <cstdio>
 #include "pointers.h"
 
 namespace LAMMPS_NS {
diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp
index 6d450f48e3..f631cc6a0a 100644
--- a/src/REPLICA/prd.cpp
+++ b/src/REPLICA/prd.cpp
@@ -15,16 +15,9 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h
-// due to OpenMPI bug which sets INT64_MAX via its mpi.h
-//   before lmptype.h can set flags to insure it is done correctly
-
-#include "lmptype.h"
-#include <mpi.h>
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "prd.h"
+#include <mpi.h>
+#include <cstring>
 #include "universe.h"
 #include "update.h"
 #include "atom.h"
@@ -40,11 +33,9 @@
 #include "fix.h"
 #include "fix_event_prd.h"
 #include "force.h"
-#include "pair.h"
 #include "random_park.h"
 #include "random_mars.h"
 #include "output.h"
-#include "dump.h"
 #include "finish.h"
 #include "timer.h"
 #include "memory.h"
diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp
index da42ba6fae..b2fbb74071 100644
--- a/src/REPLICA/tad.cpp
+++ b/src/REPLICA/tad.cpp
@@ -15,36 +15,24 @@
    Contributing author: Aidan Thompson (SNL)
 ------------------------------------------------------------------------- */
 
-// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h
-// due to OpenMPI bug which sets INT64_MAX via its mpi.h
-//   before lmptype.h can set flags to insure it is done correctly
-
-#include "lmptype.h"
+#include "tad.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "tad.h"
 #include "universe.h"
 #include "update.h"
 #include "atom.h"
 #include "domain.h"
-#include "region.h"
-#include "comm.h"
-#include "velocity.h"
 #include "integrate.h"
 #include "min.h"
 #include "neighbor.h"
 #include "modify.h"
 #include "neb.h"
 #include "compute.h"
-#include "fix.h"
 #include "fix_event_tad.h"
 #include "fix_store.h"
 #include "force.h"
-#include "pair.h"
 #include "output.h"
-#include "dump.h"
 #include "finish.h"
 #include "timer.h"
 #include "memory.h"
@@ -209,7 +197,7 @@ void TAD::command(int narg, char **arg)
   args = new char*[narg2];
   args[0] = min_style;
 
-  update->create_minimize(narg2,args);
+  update->create_minimize(narg2,args,1);
 
   delete [] args;
 
@@ -723,7 +711,7 @@ void TAD::perform_neb(int ievent)
   args = new char*[narg2];
   args[0] = min_style_neb;
 
-  update->create_minimize(narg2,args);
+  update->create_minimize(narg2,args,1);
 
   delete [] args;
 
@@ -789,7 +777,7 @@ void TAD::perform_neb(int ievent)
   args = new char*[narg2];
   args[0] = min_style;
 
-  update->create_minimize(narg2,args);
+  update->create_minimize(narg2,args,1);
 
   update->etol = etol;
   update->ftol = ftol;
diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp
index fe3e3fb993..00ca062ecc 100644
--- a/src/REPLICA/temper.cpp
+++ b/src/REPLICA/temper.cpp
@@ -15,10 +15,9 @@
    Contributing author: Mark Sears (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "temper.h"
+#include <cmath>
+#include <cstring>
 #include "universe.h"
 #include "domain.h"
 #include "atom.h"
@@ -27,14 +26,12 @@
 #include "modify.h"
 #include "compute.h"
 #include "force.h"
-#include "output.h"
-#include "thermo.h"
 #include "fix.h"
 #include "random_park.h"
 #include "finish.h"
 #include "timer.h"
-#include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -74,6 +71,10 @@ void Temper::command(int narg, char **arg)
   nevery = force->inumeric(FLERR,arg[1]);
   double temp = force->numeric(FLERR,arg[2]);
 
+  // ignore temper command, if walltime limit was already reached
+
+  if (timer->is_timeout()) return;
+
   for (whichfix = 0; whichfix < modify->nfix; whichfix++)
     if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
   if (whichfix == modify->nfix)
@@ -98,39 +99,18 @@ void Temper::command(int narg, char **arg)
   // fix style must be appropriate for temperature control, i.e. it needs
   // to provide a working Fix::reset_target() and must not change the volume.
 
-  if ((strcmp(modify->fix[whichfix]->style,"nvt") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/asphere") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/asphere/omp") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/body") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/eff") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/intel") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/kk") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/kk/host") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/kk/device") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/omp") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/sphere") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/sphere/omp") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"langevin") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"langevin/drude") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"langevin/eff") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"gld") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"gle") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"rigid/nvt") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"rigid/nvt/small") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"rigid/nvt/omp") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"rigid/nvt/small/omp") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/berendsen") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/berendsen/cuda") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/csvr") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/csld") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/rescale/cuda") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/rescale/eff") != 0))
+  if ((!utils::strmatch(modify->fix[whichfix]->style,"^nvt")) &&
+      (!utils::strmatch(modify->fix[whichfix]->style,"^langevin")) &&
+      (!utils::strmatch(modify->fix[whichfix]->style,"^gl[de]$")) &&
+      (!utils::strmatch(modify->fix[whichfix]->style,"^rigid/nvt")) &&
+      (!utils::strmatch(modify->fix[whichfix]->style,"^temp/")))
     error->universe_all(FLERR,"Tempering temperature fix is not supported");
 
   // setup for long tempering run
 
   update->whichflag = 1;
+  timer->init_timeout();
+
   update->nsteps = nsteps;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + nsteps;
@@ -237,7 +217,9 @@ void Temper::command(int narg, char **arg)
 
     // run for nevery timesteps
 
+    timer->init_timeout();
     update->integrate->run(nevery);
+    if (timer->is_timeout()) break;
 
     // compute PE
     // notify compute it will be called at next swap
diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp
index 7042fc6993..a5ed1a671d 100644
--- a/src/REPLICA/verlet_split.cpp
+++ b/src/REPLICA/verlet_split.cpp
@@ -15,7 +15,6 @@
    Contributing authors: Yuxing Peng and Chris Knight (U Chicago)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "verlet_split.h"
 #include "universe.h"
 #include "neighbor.h"
diff --git a/src/RIGID/compute_erotate_rigid.cpp b/src/RIGID/compute_erotate_rigid.cpp
index a3ddffd9ab..e15c0deb82 100644
--- a/src/RIGID/compute_erotate_rigid.cpp
+++ b/src/RIGID/compute_erotate_rigid.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
 #include "compute_erotate_rigid.h"
+#include <cstring>
 #include "update.h"
 #include "force.h"
 #include "modify.h"
diff --git a/src/RIGID/compute_ke_rigid.cpp b/src/RIGID/compute_ke_rigid.cpp
index 4de13532b2..031919b7a9 100644
--- a/src/RIGID/compute_ke_rigid.cpp
+++ b/src/RIGID/compute_ke_rigid.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
 #include "compute_ke_rigid.h"
+#include <cstring>
 #include "update.h"
 #include "force.h"
 #include "modify.h"
diff --git a/src/RIGID/compute_rigid_local.cpp b/src/RIGID/compute_rigid_local.cpp
index ec2799b6bc..57f69a64e2 100644
--- a/src/RIGID/compute_rigid_local.cpp
+++ b/src/RIGID/compute_rigid_local.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
 #include "compute_rigid_local.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp
index 1476c71d3f..a5efc22d11 100644
--- a/src/RIGID/fix_ehex.cpp
+++ b/src/RIGID/fix_ehex.cpp
@@ -22,10 +22,10 @@
    which implements the heat exchange (HEX) algorithm.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_ehex.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "region.h"
@@ -33,14 +33,9 @@
 #include "force.h"
 #include "update.h"
 #include "modify.h"
-#include "input.h"
-#include "variable.h"
 #include "memory.h"
 #include "error.h"
 #include "fix_shake.h"
-#include "neighbor.h"
-#include "comm.h"
-#include "timer.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/RIGID/fix_ehex.h b/src/RIGID/fix_ehex.h
index e29ddac135..860ed3d1f3 100644
--- a/src/RIGID/fix_ehex.h
+++ b/src/RIGID/fix_ehex.h
@@ -22,8 +22,6 @@ FixStyle(ehex,FixEHEX)
 #define LMP_FIX_EHEX_H
 
 #include "fix.h"
-#include "fix_shake.h"
-#include "region.h"
 #define EHEX_DEBUG 0
 
 namespace LAMMPS_NS {
@@ -41,9 +39,9 @@ class FixEHEX : public Fix {
   double memory_usage();
   void update_scalingmask();
   void com_properties(double *, double *, double *, double*, double *, double*);
-  bool rescale_atom(int i, Region*region);
+  bool rescale_atom(int i, class Region *region);
   virtual void grow_arrays(int nmax);
-  bool check_cluster(tagint *shake_atom, int n, Region * region);
+  bool check_cluster(tagint *shake_atom, int n, class Region *region);
 
  private:
   int iregion;
@@ -53,14 +51,14 @@ class FixEHEX : public Fix {
   char *idregion;
   int me;
 
-  double **x;              // coordinates
-  double **f;              // forces
-  double **v;              // velocities
-  double *mass;           // masses
-  double *rmass;          // reduced masses
-  int    *type;           // atom types
+  double **x;               // coordinates
+  double **f;               // forces
+  double **v;               // velocities
+  double *mass;             // masses
+  double *rmass;            // reduced masses
+  int    *type;             // atom types
   int   nlocal;             // number of local atoms
-  FixShake * fshake;        // pointer to fix_shake/fix_rattle
+  class FixShake * fshake;  // pointer to fix_shake/fix_rattle
   int constraints;          // constraints (0/1)
   int cluster;              // rescaling entire clusters (0/1)
   int hex;                  // HEX mode (0/1)
diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp
index 403f3091c6..93bf610e94 100644
--- a/src/RIGID/fix_rattle.cpp
+++ b/src/RIGID/fix_rattle.cpp
@@ -15,33 +15,22 @@
    Contributing author: Peter Wirnsberger (University of Cambridge)
 ------------------------------------------------------------------------- */
 
+#include "fix_rattle.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include <cstdio>
-#include "fix_rattle.h"
 #include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
 #include "update.h"
-#include "respa.h"
 #include "modify.h"
 #include "domain.h"
 #include "force.h"
-#include "bond.h"
-#include "angle.h"
 #include "comm.h"
-#include "group.h"
-#include "fix_respa.h"
-#include "math_const.h"
 #include "math_extra.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
-using namespace MathConst;
 using namespace MathExtra;
 
 // set RATTLE_DEBUG  1 to check constraints at end of timestep
diff --git a/src/RIGID/fix_rattle.h b/src/RIGID/fix_rattle.h
index 48edaef379..cab148f10c 100644
--- a/src/RIGID/fix_rattle.h
+++ b/src/RIGID/fix_rattle.h
@@ -20,7 +20,6 @@ FixStyle(rattle,FixRattle)
 #ifndef LMP_FIX_RATTLE_H
 #define LMP_FIX_RATTLE_H
 
-#include "fix.h"
 #include "fix_shake.h"
 
 namespace LAMMPS_NS {
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index abb669bc02..912f529403 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -11,11 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_rigid.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "fix_rigid.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
@@ -31,7 +31,6 @@
 #include "force.h"
 #include "input.h"
 #include "variable.h"
-#include "output.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp
index 4dceb1b8b4..4738e253f6 100644
--- a/src/RIGID/fix_rigid_nh.cpp
+++ b/src/RIGID/fix_rigid_nh.cpp
@@ -17,10 +17,9 @@
                Miller et al., J Chem Phys. 116, 8649-8659 (2002)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_rigid_nh.h"
+#include <cmath>
+#include <cstring>
 #include "math_extra.h"
 #include "atom.h"
 #include "compute.h"
@@ -32,7 +31,6 @@
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
-#include "output.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp
index 5016d3f168..1545e913c0 100644
--- a/src/RIGID/fix_rigid_nh_small.cpp
+++ b/src/RIGID/fix_rigid_nh_small.cpp
@@ -17,10 +17,10 @@
                Miller et al., J Chem Phys. 116, 8649-8659 (2002)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_rigid_nh_small.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "math_extra.h"
 #include "atom.h"
 #include "compute.h"
@@ -32,7 +32,6 @@
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
-#include "output.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/RIGID/fix_rigid_nph.cpp b/src/RIGID/fix_rigid_nph.cpp
index 45a4a8d09c..706e08ec12 100644
--- a/src/RIGID/fix_rigid_nph.cpp
+++ b/src/RIGID/fix_rigid_nph.cpp
@@ -17,9 +17,8 @@
                Miller et al., J Chem Phys. 116, 8649-8659 (2002)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_rigid_nph.h"
-#include "domain.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/RIGID/fix_rigid_nph_small.cpp b/src/RIGID/fix_rigid_nph_small.cpp
index d32e3043f4..32ac58220d 100644
--- a/src/RIGID/fix_rigid_nph_small.cpp
+++ b/src/RIGID/fix_rigid_nph_small.cpp
@@ -17,9 +17,8 @@
                Miller et al., J Chem Phys. 116, 8649-8659 (2002)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_rigid_nph_small.h"
-#include "domain.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/RIGID/fix_rigid_npt.cpp b/src/RIGID/fix_rigid_npt.cpp
index da5d5ffaa5..1f19fb4ec7 100644
--- a/src/RIGID/fix_rigid_npt.cpp
+++ b/src/RIGID/fix_rigid_npt.cpp
@@ -17,9 +17,8 @@
                Miller et al., J Chem Phys. 116, 8649-8659 (2002)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_rigid_npt.h"
-#include "domain.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/RIGID/fix_rigid_npt_small.cpp b/src/RIGID/fix_rigid_npt_small.cpp
index f1fd5470da..e8924be79f 100644
--- a/src/RIGID/fix_rigid_npt_small.cpp
+++ b/src/RIGID/fix_rigid_npt_small.cpp
@@ -17,9 +17,8 @@
                Miller et al., J Chem Phys. 116, 8649-8659 (2002)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_rigid_npt_small.h"
-#include "domain.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index dedd71c98d..14e230ab9c 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -11,11 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_rigid_small.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "fix_rigid_small.h"
+#include <utility>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
@@ -31,7 +32,6 @@
 #include "neighbor.h"
 #include "force.h"
 #include "input.h"
-#include "output.h"
 #include "variable.h"
 #include "random_mars.h"
 #include "math_const.h"
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index 23ced2d0e7..48a08118c5 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -11,13 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_shake.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
+#include <cctype>
 #include <cstring>
-#include <cstdio>
-#include "fix_shake.h"
-#include "fix_rattle.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp
index 2e515839c5..5e85b39076 100644
--- a/src/SHOCK/fix_append_atoms.cpp
+++ b/src/SHOCK/fix_append_atoms.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_append_atoms.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_append_atoms.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "comm.h"
diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp
index c800e8a85d..2e9f751824 100644
--- a/src/SHOCK/fix_msst.cpp
+++ b/src/SHOCK/fix_msst.cpp
@@ -17,22 +17,19 @@
    see Reed, Fried, Joannopoulos, Phys Rev Lett, 90, 235503 (2003)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "fix_msst.h"
+#include <mpi.h>
+#include <cstring>
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
-#include "output.h"
 #include "modify.h"
 #include "fix_external.h"
 #include "compute.h"
 #include "kspace.h"
 #include "update.h"
-#include "respa.h"
 #include "domain.h"
-#include "thermo.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp
index c6df6646cf..8ad787d759 100644
--- a/src/SHOCK/fix_nphug.cpp
+++ b/src/SHOCK/fix_nphug.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "fix_nphug.h"
+#include <cstring>
+#include <cmath>
 #include "modify.h"
 #include "error.h"
 #include "update.h"
@@ -22,8 +21,6 @@
 #include "force.h"
 #include "domain.h"
 #include "group.h"
-#include "memory.h"
-#include "comm.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp
index eb89e19517..5a359d9f6f 100644
--- a/src/SHOCK/fix_wall_piston.cpp
+++ b/src/SHOCK/fix_wall_piston.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_wall_piston.h"
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_wall_piston.h"
 #include "atom.h"
-#include "modify.h"
 #include "domain.h"
 #include "lattice.h"
 #include "update.h"
diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp
index cc7a84281e..7ca9d52467 100644
--- a/src/SNAP/compute_sna_atom.cpp
+++ b/src/SNAP/compute_sna_atom.cpp
@@ -10,10 +10,11 @@
 
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
-#include "sna.h"
+
+#include "compute_sna_atom.h"
 #include <cstring>
 #include <cstdlib>
-#include "compute_sna_atom.h"
+#include "sna.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp
index 0a82cdeb00..7744a23612 100644
--- a/src/SNAP/compute_snad_atom.cpp
+++ b/src/SNAP/compute_snad_atom.cpp
@@ -10,10 +10,11 @@
 
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
-#include "sna.h"
+
+#include "compute_snad_atom.h"
 #include <cstring>
 #include <cstdlib>
-#include "compute_snad_atom.h"
+#include "sna.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp
index 374bf32298..c26edf36e0 100644
--- a/src/SNAP/compute_snav_atom.cpp
+++ b/src/SNAP/compute_snav_atom.cpp
@@ -10,10 +10,11 @@
 
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
-#include "sna.h"
+
+#include "compute_snav_atom.h"
 #include <cstring>
 #include <cstdlib>
-#include "compute_snav_atom.h"
+#include "sna.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
@@ -21,7 +22,6 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "force.h"
-#include "pair.h"
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp
index 4dce39361f..59b333fa31 100644
--- a/src/SNAP/pair_snap.cpp
+++ b/src/SNAP/pair_snap.cpp
@@ -11,24 +11,21 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "pair_snap.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "pair_snap.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "force.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "sna.h"
-#include "domain.h"
 #include "memory.h"
 #include "error.h"
 
-#include <cmath>
-
 using namespace LAMMPS_NS;
 
 #define MAXLINE 1024
diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp
index 985110bdee..01d2d12b8f 100644
--- a/src/SNAP/sna.cpp
+++ b/src/SNAP/sna.cpp
@@ -18,14 +18,8 @@
 #include "sna.h"
 #include <cmath>
 #include "math_const.h"
-#include "math_extra.h"
-#include <cstring>
-#include <cstdlib>
-
 #include "memory.h"
 #include "error.h"
-#include "comm.h"
-#include "atom.h"
 
 using namespace std;
 using namespace LAMMPS_NS;
diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp
index 8cc38dbc15..ad1384ffd2 100644
--- a/src/SPIN/atom_vec_spin.cpp
+++ b/src/SPIN/atom_vec_spin.cpp
@@ -23,16 +23,14 @@
    and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */
 
+#include "atom_vec_spin.h"
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
-#include "atom_vec_spin.h"
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
 #include "fix.h"
-#include "force.h"
 #include "memory.h"
 #include "modify.h"
 #include "utils.h"
diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp
index 501b708c88..1f808eb1bd 100644
--- a/src/SPIN/compute_spin.cpp
+++ b/src/SPIN/compute_spin.cpp
@@ -21,21 +21,17 @@
    and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
-#include "atom.h"
 #include "compute_spin.h"
-#include "domain.h"
+#include <mpi.h>
+#include <cmath>
+#include "atom.h"
 #include "error.h"
 #include "force.h"
-#include "math_special.h"
 #include "math_const.h"
 #include "memory.h"
-#include "modify.h"
 #include "update.h"
 
 using namespace LAMMPS_NS;
-using namespace MathSpecial;
 using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp
index ec6f719a77..ec9c98c4f8 100644
--- a/src/SPIN/fix_langevin_spin.cpp
+++ b/src/SPIN/fix_langevin_spin.cpp
@@ -21,31 +21,19 @@
    and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
+#include "fix_langevin_spin.h"
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-
-#include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "comm.h"
-#include "compute.h"
-#include "domain.h"
 #include "error.h"
-#include "fix_langevin_spin.h"
 #include "force.h"
-#include "group.h"
-#include "input.h"
 #include "math_const.h"
-#include "math_extra.h"
 #include "memory.h"
 #include "modify.h"
-#include "random_mars.h"
 #include "random_park.h"
-#include "region.h"
 #include "respa.h"
 #include "update.h"
-#include "variable.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -142,13 +130,11 @@ void FixLangevinSpin::init()
 
 void FixLangevinSpin::setup(int vflag)
 {
-  if (strstr(update->integrate_style,"verlet"))
-    post_force(vflag);
-  else {
+  if (utils::strmatch(update->integrate_style,"^respa")) {
     ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
     post_force_respa(vflag,nlevels_respa-1,0);
     ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
-  }
+  } else post_force(vflag);
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp
index a8cb0cd2ca..5acbbf59e8 100644
--- a/src/SPIN/fix_neb_spin.cpp
+++ b/src/SPIN/fix_neb_spin.cpp
@@ -21,15 +21,13 @@
    Computer Physics Communications, 196, 335-347.
 ------------------------------------------------------------------------- */
 
+#include "fix_neb_spin.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "fix_neb_spin.h"
 #include "universe.h"
 #include "update.h"
 #include "atom.h"
-#include "domain.h"
 #include "comm.h"
 #include "modify.h"
 #include "compute.h"
@@ -37,11 +35,9 @@
 #include "memory.h"
 #include "error.h"
 #include "force.h"
-#include "math_const.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
-using namespace MathConst;
 
 enum{SINGLE_PROC_DIRECT,SINGLE_PROC_MAP,MULTI_PROC};
 
diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp
index b992f17cc3..b1b466b5a4 100644
--- a/src/SPIN/fix_nve_spin.cpp
+++ b/src/SPIN/fix_nve_spin.cpp
@@ -21,38 +21,24 @@
    and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
+#include "fix_nve_spin.h"
 #include <cstring>
-
 #include "atom.h"
-#include "atom_vec.h"
 #include "citeme.h"
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_nve_spin.h"
 #include "fix_precession_spin.h"
 #include "fix_langevin_spin.h"
 #include "fix_setforce_spin.h"
 #include "force.h"
-#include "math_vector.h"
-#include "math_extra.h"
-#include "math_const.h"
 #include "memory.h"
 #include "modify.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "pair.h"
-#include "pair_hybrid.h"
 #include "pair_spin.h"
-#include "respa.h"
 #include "update.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
-using namespace MathConst;
-using namespace MathExtra;
 
 static const char cite_fix_nve_spin[] =
   "fix nve/spin command:\n\n"
diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h
index 4800575c06..1e3b87c1fb 100644
--- a/src/SPIN/fix_nve_spin.h
+++ b/src/SPIN/fix_nve_spin.h
@@ -21,8 +21,6 @@ FixStyle(nve/spin,FixNVESpin)
 #define LMP_FIX_NVE_SPIN_H
 
 #include "fix.h"
-#include "pair.h"
-#include "pair_spin.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp
index 1ea134d367..3296b28228 100644
--- a/src/SPIN/fix_precession_spin.cpp
+++ b/src/SPIN/fix_precession_spin.cpp
@@ -21,21 +21,16 @@
    and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */
 
+#include "fix_precession_spin.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
 #include "error.h"
-#include "domain.h"
-#include "error.h"
-#include "fix_precession_spin.h"
 #include "force.h"
 #include "input.h"
 #include "math_const.h"
-#include "memory.h"
 #include "modify.h"
-#include "neigh_list.h"
 #include "respa.h"
 #include "update.h"
 #include "variable.h"
diff --git a/src/SPIN/fix_setforce_spin.cpp b/src/SPIN/fix_setforce_spin.cpp
index c2807418ec..e36a9d260d 100644
--- a/src/SPIN/fix_setforce_spin.cpp
+++ b/src/SPIN/fix_setforce_spin.cpp
@@ -21,20 +21,15 @@
    and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "fix_setforce_spin.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "domain.h"
 #include "region.h"
-#include "respa.h"
 #include "input.h"
 #include "variable.h"
 #include "memory.h"
-#include "error.h"
-#include "force.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp
index dda414ff97..553526ea8e 100644
--- a/src/SPIN/min_spin.cpp
+++ b/src/SPIN/min_spin.cpp
@@ -17,11 +17,10 @@
    Please cite the related publication:
 ------------------------------------------------------------------------- */
 
+#include "min_spin.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "min_spin.h"
 #include "universe.h"
 #include "atom.h"
 #include "force.h"
@@ -29,8 +28,6 @@
 #include "output.h"
 #include "timer.h"
 #include "error.h"
-#include "modify.h"
-#include "math_special.h"
 #include "math_const.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp
index 46a0541488..2bcfe6573a 100644
--- a/src/SPIN/neb_spin.cpp
+++ b/src/SPIN/neb_spin.cpp
@@ -21,18 +21,12 @@
    Computer Physics Communications, 196, 335-347.
 ------------------------------------------------------------------------- */
 
-// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h
-// due to OpenMPI bug which sets INT64_MAX via its mpi.h
-// before lmptype.h can set flags to insure it is done correctly
-
-#include "lmptype.h"
+#include "neb_spin.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "neb_spin.h"
 #include "citeme.h"
-#include "compute.h"
 #include "force.h"
 #include "universe.h"
 #include "atom.h"
@@ -49,10 +43,8 @@
 #include "timer.h"
 #include "memory.h"
 #include "error.h"
-#include "math_const.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 static const char cite_neb_spin[] =
   "neb/spin command:\n\n"
diff --git a/src/SPIN/neb_spin.h b/src/SPIN/neb_spin.h
index c128eaffa4..568eca0957 100644
--- a/src/SPIN/neb_spin.h
+++ b/src/SPIN/neb_spin.h
@@ -20,7 +20,6 @@ CommandStyle(neb/spin,NEBSpin)
 #ifndef LMP_NEB_SPIN_H
 #define LMP_NEB_SPIN_H
 
-#include <cstdio>
 #include "pointers.h"
 
 namespace LAMMPS_NS {
diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp
index 929b79bef3..fef247c09b 100644
--- a/src/SPIN/pair_spin.cpp
+++ b/src/SPIN/pair_spin.cpp
@@ -21,26 +21,15 @@
    and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
+#include "pair_spin.h"
 #include <cstring>
-
 #include "atom.h"
-#include "comm.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_nve_spin.h"
 #include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
 #include "math_const.h"
-#include "memory.h"
 #include "modify.h"
 #include "pair.h"
-#include "pair_hybrid.h"
-#include "pair_hybrid_overlay.h"
-#include "pair_spin.h"
 #include "update.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h
index 1be8550c65..3a909e1d13 100644
--- a/src/SPIN/pair_spin.h
+++ b/src/SPIN/pair_spin.h
@@ -14,7 +14,7 @@
 #ifndef LMP_PAIR_SPIN_H
 #define LMP_PAIR_SPIN_H
 
-#include "pair.h"
+#include "pair.h"  // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp
index 4ff198488a..fb0ec8bb20 100644
--- a/src/SPIN/pair_spin_dipole_cut.cpp
+++ b/src/SPIN/pair_spin_dipole_cut.cpp
@@ -21,16 +21,16 @@
    and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_spin_dipole_cut.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
+#include "fix.h"
 #include "fix_nve_spin.h"
 #include "force.h"
 #include "math_const.h"
diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp
index e3575a6a07..670fccfce2 100644
--- a/src/SPIN/pair_spin_dipole_long.cpp
+++ b/src/SPIN/pair_spin_dipole_long.cpp
@@ -13,20 +13,19 @@
 
 /* ------------------------------------------------------------------------
    Contributing authors: Julien Tranchida (SNL)
-			 Stan Moore (SNL)
+                         Stan Moore (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-
 #include "pair_spin_dipole_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
+#include "fix.h"
 #include "fix_nve_spin.h"
 #include "force.h"
 #include "kspace.h"
@@ -59,12 +58,12 @@ lockfixnvespin(NULL)
   no_virial_fdotr_compute = 1;
   lattice_flag = 0;
 
-  hbar = force->hplanck/MY_2PI;			// eV/(rad.THz)
+  hbar = force->hplanck/MY_2PI;                 // eV/(rad.THz)
   mub = 9.274e-4;                               // in A.Ang^2
   mu_0 = 785.15;                                // in eV/Ang/A^2
   mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);     // in eV.Ang^3
-  //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);	// in eV
-  mub2mu0hbinv = mub2mu0 / hbar;		// in rad.THz
+  //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI);   // in eV
+  mub2mu0hbinv = mub2mu0 / hbar;                // in rad.THz
 
 }
 
@@ -243,7 +242,7 @@ void PairSpinDipoleLong::compute(int eflag, int vflag)
   double **x = atom->x;
   double **f = atom->f;
   double **fm = atom->fm;
-  double **sp = atom->sp;	
+  double **sp = atom->sp;       
   int *type = atom->type;  
   int nlocal = atom->nlocal;  
   int newton_pair = force->newton_pair;
@@ -314,36 +313,36 @@ void PairSpinDipoleLong::compute(int eflag, int vflag)
         bij[2] = (3.0*bij[1] + pre2*expm2) * r2inv;
         bij[3] = (5.0*bij[2] + pre3*expm2) * r2inv;
 
-	compute_long(i,j,eij,bij,fmi,spi,spj);
-	compute_long_mech(i,j,eij,bij,fmi,spi,spj);
+        compute_long(i,j,eij,bij,fmi,spi,spj);
+        compute_long_mech(i,j,eij,bij,fmi,spi,spj);
       }
 
       // force accumulation
 
-      f[i][0] += fi[0];	 
-      f[i][1] += fi[1];	  	  
+      f[i][0] += fi[0];  
+      f[i][1] += fi[1];           
       f[i][2] += fi[2];
-      fm[i][0] += fmi[0];	 
-      fm[i][1] += fmi[1];	  	  
+      fm[i][0] += fmi[0];        
+      fm[i][1] += fmi[1];                 
       fm[i][2] += fmi[2];
 
       if (newton_pair || j < nlocal) {
-	f[j][0] -= fi[0];	 
-        f[j][1] -= fi[1];	  	  
+        f[j][0] -= fi[0];        
+        f[j][1] -= fi[1];                 
         f[j][2] -= fi[2];
       }
 
       if (eflag) {
-	if (rsq <= local_cut2) {
-	  evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] + 
-	    spi[2]*fmi[2];
-	  evdwl *= hbar;
-	}
+        if (rsq <= local_cut2) {
+          evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] + 
+            spi[2]*fmi[2];
+          evdwl *= hbar;
+        }
       } else evdwl = 0.0;
 
 
       if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
-	  evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]);
+          evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]);
 
     }
   }
@@ -365,7 +364,7 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3])
 
   int *type = atom->type;  
   double **x = atom->x;
-  double **sp = atom->sp;	
+  double **sp = atom->sp;       
   double **fm_long = atom->fm_long;
 
   ilist = list->ilist;
@@ -550,7 +549,7 @@ void PairSpinDipoleLong::write_restart(FILE *fp)
     for (j = i; j <= atom->ntypes; j++) {
       fwrite(&setflag[i][j],sizeof(int),1,fp);
       if (setflag[i][j]) {
-	fwrite(&cut_spin_long[i][j],sizeof(int),1,fp);
+        fwrite(&cut_spin_long[i][j],sizeof(int),1,fp);
       }
     }
   }
@@ -573,10 +572,10 @@ void PairSpinDipoleLong::read_restart(FILE *fp)
       if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
-	if (me == 0) {
-	  fread(&cut_spin_long[i][j],sizeof(int),1,fp);
-	}
-	MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world);
+        if (me == 0) {
+          fread(&cut_spin_long[i][j],sizeof(int),1,fp);
+        }
+        MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world);
       }
     }
   }
diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp
index 41430d230f..afd2deaa6a 100644
--- a/src/SPIN/pair_spin_dmi.cpp
+++ b/src/SPIN/pair_spin_dmi.cpp
@@ -21,28 +21,24 @@
    and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */
 
+#include "pair_spin_dmi.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-
 #include "atom.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "fix.h"
 #include "fix_nve_spin.h"
-#include "pair_hybrid.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "math_const.h"
 #include "memory.h"
 #include "modify.h"
-#include "pair_spin_dmi.h"
 #include "update.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp
index 93b6d9501e..cc28018ad0 100644
--- a/src/SPIN/pair_spin_exchange.cpp
+++ b/src/SPIN/pair_spin_exchange.cpp
@@ -21,28 +21,24 @@
    and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */
 
+#include "pair_spin_exchange.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-
 #include "atom.h"
 #include "comm.h"
 #include "error.h"
 #include "fix.h"
 #include "fix_nve_spin.h"
 #include "force.h"
-#include "pair_hybrid.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "math_const.h"
 #include "memory.h"
 #include "modify.h"
-#include "pair_spin_exchange.h"
 #include "update.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp
index 1f1488b93c..6756ebc3cc 100644
--- a/src/SPIN/pair_spin_magelec.cpp
+++ b/src/SPIN/pair_spin_magelec.cpp
@@ -21,28 +21,24 @@
    and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */
 
+#include "pair_spin_magelec.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-
 #include "atom.h"
 #include "comm.h"
 #include "error.h"
 #include "fix.h"
 #include "fix_nve_spin.h"
 #include "force.h"
-#include "pair_hybrid.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "math_const.h"
 #include "memory.h"
 #include "modify.h"
-#include "pair_spin_magelec.h"
 #include "update.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp
index 03041da17f..355ba20f39 100644
--- a/src/SPIN/pair_spin_neel.cpp
+++ b/src/SPIN/pair_spin_neel.cpp
@@ -21,29 +21,24 @@
    and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */
 
+#include "pair_spin_neel.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-
 #include "atom.h"
 #include "comm.h"
 #include "error.h"
-#include "force.h"
 #include "fix.h"
 #include "fix_nve_spin.h"
 #include "force.h"
-#include "pair_hybrid.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "math_const.h"
 #include "memory.h"
 #include "modify.h"
-#include "pair_spin_neel.h"
 #include "update.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp
index d87d2b5e56..d5eec91f50 100644
--- a/src/SRD/fix_srd.cpp
+++ b/src/SRD/fix_srd.cpp
@@ -15,10 +15,10 @@
    Contributing authors: Jeremy Lechman (SNL), Pieter in 't Veld (BASF)
 ------------------------------------------------------------------------- */
 
+#include "fix_srd.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_srd.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
@@ -27,7 +27,6 @@
 #include "group.h"
 #include "update.h"
 #include "force.h"
-#include "pair.h"
 #include "domain.h"
 #include "neighbor.h"
 #include "comm.h"
diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp
index 24b0c3cec5..ab113df28a 100644
--- a/src/SRD/fix_wall_srd.cpp
+++ b/src/SRD/fix_wall_srd.cpp
@@ -11,11 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_wall_srd.h"
-#include "atom.h"
-#include "modify.h"
+#include <mpi.h>
+#include <cstring>
 #include "fix.h"
 #include "domain.h"
 #include "lattice.h"
diff --git a/src/STUBS/Makefile b/src/STUBS/Makefile
index 3649ddb383..3c3c3b46d9 100644
--- a/src/STUBS/Makefile
+++ b/src/STUBS/Makefile
@@ -28,7 +28,7 @@ ARCHFLAG =	rs
 
 # Targets
 
-lib:	$(OBJ)
+$(EXE):	$(OBJ)
 	$(ARCHIVE) $(ARCHFLAG) $(EXE) $(OBJ)
 
 clean:
@@ -41,4 +41,4 @@ clean:
 
 # Individual dependencies
 
-$(OBJ):	$(INC)
+$(OBJ):	$(INC) ../version.h
diff --git a/src/STUBS/mpi.c b/src/STUBS/mpi.c
index cd92750b9a..f56d3616c8 100644
--- a/src/STUBS/mpi.c
+++ b/src/STUBS/mpi.c
@@ -20,6 +20,7 @@
 #include <stdint.h>
 #include <sys/time.h>
 #include <mpi.h>
+#include "../version.h"
 
 /* data structure for double/int */
 
@@ -80,7 +81,7 @@ int MPI_Finalized(int *flag)
 
 int MPI_Get_library_version(char *version, int *resultlen)
 {
-  const char string[] = "LAMMPS MPI STUBS";
+  const char string[] = "LAMMPS MPI STUBS for LAMMPS version " LAMMPS_VERSION;
   int len;
 
   if (!version || !resultlen) return MPI_ERR_ARG;
diff --git a/src/USER-ADIOS/dump_atom_adios.cpp b/src/USER-ADIOS/dump_atom_adios.cpp
index 55d6c5fbf9..e711b8a583 100644
--- a/src/USER-ADIOS/dump_atom_adios.cpp
+++ b/src/USER-ADIOS/dump_atom_adios.cpp
@@ -16,6 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "dump_atom_adios.h"
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "error.h"
@@ -23,7 +24,6 @@
 #include "memory.h"
 #include "universe.h"
 #include "update.h"
-#include <cstring>
 
 #include "adios2.h"
 
diff --git a/src/USER-ADIOS/dump_custom_adios.cpp b/src/USER-ADIOS/dump_custom_adios.cpp
index 67f3deeb64..ee6d7d7e49 100644
--- a/src/USER-ADIOS/dump_custom_adios.cpp
+++ b/src/USER-ADIOS/dump_custom_adios.cpp
@@ -16,6 +16,8 @@
 ------------------------------------------------------------------------- */
 
 #include "dump_custom_adios.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "compute.h"
 #include "domain.h"
@@ -30,8 +32,6 @@
 #include "universe.h"
 #include "update.h"
 #include "variable.h"
-#include <cmath>
-#include <cstring>
 
 #include "adios2.h"
 
diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp
index f53343ced1..e2a1768f55 100644
--- a/src/USER-ATC/fix_atc.cpp
+++ b/src/USER-ATC/fix_atc.cpp
@@ -11,8 +11,10 @@
    See the README file in the top-level LAMMPS directory.
    ------------------------------------------------------------------------- */
 
-// LAMMPS
 #include "fix_atc.h"
+#include <cstdio>
+#include <cstring>
+#include <sstream>
 #include "fix_nve.h"
 #include "atom.h"
 #include "force.h"
@@ -24,7 +26,7 @@
 #include "pointers.h"
 #include "comm.h"
 #include "group.h"
-// ATC
+
 #include "ATC_Method.h"
 #include "ATC_Transfer.h"
 #include "ATC_TransferKernel.h"
@@ -34,10 +36,6 @@
 #include "ATC_CouplingMass.h"
 #include "ATC_CouplingMomentumEnergy.h"
 #include "LammpsInterface.h"
-// other
-#include <cstdio>
-#include <cstring>
-#include <sstream>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp
index bffe49e6c5..bce334a7b3 100644
--- a/src/USER-AWPMD/atom_vec_wavepacket.cpp
+++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp
@@ -15,15 +15,12 @@
    Contributing author: Ilya Valuev (JIHT, Moscow, Russia)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "atom_vec_wavepacket.h"
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
 #include "modify.h"
-#include "force.h"
 #include "fix.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp
index 7722c93121..a147a11081 100644
--- a/src/USER-AWPMD/fix_nve_awpmd.cpp
+++ b/src/USER-AWPMD/fix_nve_awpmd.cpp
@@ -15,15 +15,14 @@
    Contributing author: Ilya Valuev (JIHT, Moscow, Russia)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_awpmd.h"
+#include "pair_awpmd_cut.h"
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "respa.h"
 #include "error.h"
+#include "utils.h"
 
 #include "TCP/wpmd_split.h"
 
@@ -62,7 +61,7 @@ void FixNVEAwpmd::init()
   dtv = update->dt;
   dtf = 0.5 * update->dt * force->ftm2v;
 
-  if (strstr(update->integrate_style,"respa"))
+  if (utils::strmatch(update->integrate_style,"^respa"))
     step_respa = ((Respa *) update->integrate)->step;
 
   awpmd_pair=(PairAWPMDCut *)force->pair;
diff --git a/src/USER-AWPMD/fix_nve_awpmd.h b/src/USER-AWPMD/fix_nve_awpmd.h
index 140d234308..832f5821a3 100644
--- a/src/USER-AWPMD/fix_nve_awpmd.h
+++ b/src/USER-AWPMD/fix_nve_awpmd.h
@@ -25,7 +25,6 @@ FixStyle(nve/awpmd,FixNVEAwpmd)
 #define LMP_FIX_NVE_awpmd_H
 
 #include "fix.h"
-#include "pair_awpmd_cut.h"
 
 namespace LAMMPS_NS {
 
@@ -45,7 +44,7 @@ class FixNVEAwpmd : public Fix {
   double *step_respa;
   int mass_require;
 
-  PairAWPMDCut *awpmd_pair;
+  class PairAWPMDCut *awpmd_pair;
 };
 
 }
diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp
index 1b7bf35c28..75ebb0e251 100644
--- a/src/USER-AWPMD/pair_awpmd_cut.cpp
+++ b/src/USER-AWPMD/pair_awpmd_cut.cpp
@@ -15,11 +15,12 @@
    Contributing author: Ilya Valuev (JIHT, Moscow, Russia)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_awpmd_cut.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <map>
+#include <utility>
 #include "atom.h"
 #include "update.h"
 #include "min.h"
@@ -32,6 +33,9 @@
 #include "memory.h"
 #include "error.h"
 
+#include "logexc.h"
+#include "vector_3.h"
+#include "TCP/wpmd.h"
 #include "TCP/wpmd_split.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp
index c43910ec6d..d0a24b99a3 100644
--- a/src/USER-BOCS/compute_pressure_bocs.cpp
+++ b/src/USER-BOCS/compute_pressure_bocs.cpp
@@ -14,10 +14,11 @@
    from The Pennsylvania State University
 ------------------------------------------------------------------------- */
 
+#include "compute_pressure_bocs.h"
 #include <mpi.h>
+#include <cmath>
 #include <cstring>
 #include <cstdlib>
-#include "compute_pressure_bocs.h"
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp
index 7bdb8933e3..adce231bf1 100644
--- a/src/USER-BOCS/fix_bocs.cpp
+++ b/src/USER-BOCS/fix_bocs.cpp
@@ -14,11 +14,10 @@
    from The Pennsylvania State University
 ------------------------------------------------------------------------- */
 
+#include "fix_bocs.h"
 #include <cstring>
 #include <cstdlib>
 #include <cmath>
-#include "fix_bocs.h"
-#include "math_extra.h"
 #include "atom.h"
 #include "force.h"
 #include "group.h"
@@ -60,6 +59,9 @@ enum{NOBIAS,BIAS};
 enum{NONE,XYZ,XY,YZ,XZ};
 enum{ISO,ANISO,TRICLINIC};
 
+// NB: Keep error and warning messages less than 255 chars long.
+const int MAX_MESSAGE_LENGTH = 256;
+
 /* ----------------------------------------------------------------------
    NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
  ---------------------------------------------------------------------- */
@@ -631,24 +633,32 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
   double **data = (double **) calloc(N_columns,sizeof(double *));
   char * line = (char *) calloc(200,sizeof(char));
 
+  bool badInput = false;
+  char badDataMsg[MAX_MESSAGE_LENGTH];
   fpi = fopen(filename,"r");
   if (fpi)
   {
     while (fgets(line,199,fpi)) { ++n_entries; }
-    fclose(fpi);
+
     for (i = 0; i < N_columns; ++i)
     {
       data[i] = (double *) calloc(n_entries,sizeof(double));
     }
-  } else {
-    char errmsg[128];
-    snprintf(errmsg,128,"Unable to open file: %s\n",filename);
-    error->all(FLERR,errmsg);
-  }
 
-  n_entries = 0;
-  fpi = fopen(filename,"r");
-  if (fpi) {
+    // Don't need to re-open the file to make a second pass through it
+    // simply rewind to beginning
+    rewind(fpi);
+
+    double stdVolumeInterval = 0.0;
+    double currVolumeInterval = 0.0;
+    // When comparing doubles/floats, we need an Epsilon.
+    // The literature indicates getting this value right in the
+    // general case can be pretty complicated. I don't think it
+    // needs to be complicated here, though. At least based on the
+    // sample data I've seen where the volume values are fairly
+    // large.
+    const double volumeIntervalTolerance = 0.001;
+    n_entries = 0;
     while( fgets(line,199,fpi)) {
       ++n_entries;
       test_sscanf = sscanf(line," %f , %f ",&f1, &f2);
@@ -656,19 +666,47 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
       {
         data[0][n_entries-1] = (double) f1;
         data[1][n_entries-1] = (double) f2;
+        if (n_entries == 2) {
+          stdVolumeInterval = data[0][n_entries-1] - data[0][n_entries-2];
+        }
+        else if (n_entries > 2) {
+          currVolumeInterval = data[0][n_entries-1] - data[0][n_entries-2];
+          if (fabs(currVolumeInterval - stdVolumeInterval) > volumeIntervalTolerance) {
+            snprintf(badDataMsg,MAX_MESSAGE_LENGTH,
+                     "BAD VOLUME INTERVAL: spline analysis requires uniform"
+                     " volume distribution, found inconsistent volume"
+                     " differential, line %d of file %s\n\tline: %s",
+                     n_entries,filename,line);
+            error->message(FLERR,badDataMsg);
+            badInput = true;
+          }
+        }
+        // no else -- first entry is simply ignored
       }
       else
       {
-        fprintf(stderr,"WARNING: did not find 2 comma separated values in "
-                 "line %d of file %s\n\tline: %s",n_entries,filename,line);
+        snprintf(badDataMsg,MAX_MESSAGE_LENGTH,
+                 "BAD INPUT FORMAT: did not find 2 comma separated numeric"
+                 " values in line %d of file %s\n\tline: %s",
+                 n_entries,filename,line);
+        error->message(FLERR,badDataMsg);
+        badInput = true;
       }
     }
-  } else {
-    char errmsg[128];
-    snprintf(errmsg,128,"Unable to open file: %s\n",filename);
+    fclose(fpi);
+  }
+  else {
+    char errmsg[MAX_MESSAGE_LENGTH];
+    snprintf(errmsg,MAX_MESSAGE_LENGTH,"Unable to open file: %s\n",filename);
+    error->all(FLERR,errmsg);
+  }
+
+  if (badInput) {
+    char errmsg[MAX_MESSAGE_LENGTH];
+    snprintf(errmsg,MAX_MESSAGE_LENGTH,
+             "Bad volume / pressure-correction data: %s\nSee details above",filename);
     error->all(FLERR,errmsg);
   }
-  fclose(fpi);
 
   if (p_basis_type == 1)
   {
@@ -692,9 +730,10 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
   }
   else
   {
-    char * errmsg = (char *) calloc(70,sizeof(char));
-    sprintf(errmsg,"ERROR: invalid p_basis_type value "
-                                    "of %d in read_F_table",p_basis_type);
+    char errmsg[MAX_MESSAGE_LENGTH];
+    snprintf(errmsg, MAX_MESSAGE_LENGTH,
+             "ERROR: invalid p_basis_type value of %d in read_F_table",
+             p_basis_type);
     error->all(FLERR,errmsg);
   }
   // cleanup
diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/USER-CGDNA/bond_oxdna2_fene.cpp
index 557d62aac6..682f325345 100644
--- a/src/USER-CGDNA/bond_oxdna2_fene.cpp
+++ b/src/USER-CGDNA/bond_oxdna2_fene.cpp
@@ -14,8 +14,6 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "bond_oxdna2_fene.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp
index 9d6453f5a8..f549fc423d 100644
--- a/src/USER-CGDNA/bond_oxdna_fene.cpp
+++ b/src/USER-CGDNA/bond_oxdna_fene.cpp
@@ -14,12 +14,11 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "bond_oxdna_fene.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/USER-CGDNA/fix_nve_dot.cpp
index 72b3388793..ff8e1c0ee2 100644
--- a/src/USER-CGDNA/fix_nve_dot.cpp
+++ b/src/USER-CGDNA/fix_nve_dot.cpp
@@ -14,16 +14,11 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_dot.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
-#include "force.h"
 #include "update.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
index c73801c97a..59def4c812 100644
--- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
+++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
@@ -15,10 +15,9 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_dotc_langevin.h"
+#include <cmath>
+#include <cstring>
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
@@ -26,7 +25,6 @@
 #include "update.h"
 #include "comm.h"
 #include "random_mars.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-CGDNA/mf_oxdna.h b/src/USER-CGDNA/mf_oxdna.h
index c63a37cde2..e4ed1bbd03 100644
--- a/src/USER-CGDNA/mf_oxdna.h
+++ b/src/USER-CGDNA/mf_oxdna.h
@@ -14,7 +14,6 @@
 #ifndef MF_OXDNA_H
 #define MF_OXDNA_H
 
-#include <cstdio>
 #include "math_extra.h"
 
 namespace MFOxdna {
diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
index 4fde5e37b4..609b63e27f 100644
--- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
@@ -14,20 +14,16 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_oxdna2_coaxstk.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "mf_oxdna.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp
index ca5f44b815..630dd7a559 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp
@@ -14,29 +14,21 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_oxdna2_dh.h"
-#include "mf_oxdna.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
-using namespace MFOxdna;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/USER-CGDNA/pair_oxdna2_excv.cpp
index f2fb77b3b2..d8a263676f 100644
--- a/src/USER-CGDNA/pair_oxdna2_excv.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_excv.cpp
@@ -14,10 +14,6 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_oxdna2_excv.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
index 6b10117f91..d71acc2029 100644
--- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
@@ -14,20 +14,16 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_oxdna_coaxstk.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "mf_oxdna.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp
index ddfe32946c..f187fc7403 100644
--- a/src/USER-CGDNA/pair_oxdna_excv.cpp
+++ b/src/USER-CGDNA/pair_oxdna_excv.cpp
@@ -14,28 +14,22 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_oxdna_excv.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "mf_oxdna.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace MFOxdna;
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp
index 03e83e1324..e9852d0e38 100644
--- a/src/USER-CGDNA/pair_oxdna_hbond.cpp
+++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp
@@ -14,28 +14,22 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_oxdna_hbond.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "mf_oxdna.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace MFOxdna;
 
 // sequence-specific base-pairing strength
diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp
index 3c7a3f05bc..3d0c4e9136 100644
--- a/src/USER-CGDNA/pair_oxdna_stk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_stk.cpp
@@ -14,28 +14,22 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_oxdna_stk.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <utility>
 #include "mf_oxdna.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "atom_vec_ellipsoid.h"
 #include "math_extra.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace MFOxdna;
 
 // sequence-specific stacking strength
diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp
index d5248937ca..95f5694818 100644
--- a/src/USER-CGDNA/pair_oxdna_xstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp
@@ -14,20 +14,16 @@
    Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_oxdna_xstk.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "mf_oxdna.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp
index 823c725e07..862c165bbd 100644
--- a/src/USER-CGSDK/angle_sdk.cpp
+++ b/src/USER-CGSDK/angle_sdk.cpp
@@ -18,9 +18,9 @@
    lj/sdk potential for coarse grained MD simulations.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_sdk.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "pair.h"
diff --git a/src/USER-CGSDK/angle_sdk.h b/src/USER-CGSDK/angle_sdk.h
index 293004ad4d..2e94b44470 100644
--- a/src/USER-CGSDK/angle_sdk.h
+++ b/src/USER-CGSDK/angle_sdk.h
@@ -20,7 +20,6 @@ AngleStyle(sdk,AngleSDK)
 #ifndef LMP_ANGLE_SDK_H
 #define LMP_ANGLE_SDK_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp
index 7dd6c04436..1301dc4155 100644
--- a/src/USER-CGSDK/pair_lj_sdk.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk.cpp
@@ -16,20 +16,14 @@
    This style is a simplified re-implementation of the CG/CMM pair style
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_sdk.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
@@ -37,7 +31,6 @@
 #include "lj_sdk_common.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace LJSDKParms;
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
index 33a1659df9..62acf00d27 100644
--- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
@@ -16,21 +16,16 @@
    This style is a simplified re-implementation of the CG/CMM pair style
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_sdk_coul_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
@@ -38,7 +33,6 @@
 #include "lj_sdk_common.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace LJSDKParms;
 
 #define EWALD_F   1.12837917
diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp
index d26f8efcdc..f168089fae 100644
--- a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp
@@ -16,28 +16,18 @@
    This style is a simplified re-implementation of the CG/CMM pair style
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_sdk_coul_msm.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
 #include "kspace.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "math_const.h"
-#include "memory.h"
 #include "error.h"
 
 #include "lj_sdk_common.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace LJSDKParms;
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp
index 651999f79c..2c43a3fb26 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.cpp
+++ b/src/USER-COLVARS/colvarproxy_lammps.cpp
@@ -8,33 +8,22 @@
 // Colvars repository at GitHub.
 
 
+#include "colvarproxy_lammps.h"
 #include <mpi.h>
+#include <sys/stat.h>
+#include <cerrno>
+#include <cstring>
+#include <iostream>
+#include <memory>
+#include <string>
+
 #include "lammps.h"
-#include "atom.h"
 #include "error.h"
 #include "output.h"
 #include "random_park.h"
 
-#include "fix_colvars.h"
-
 #include "colvarmodule.h"
-#include "colvar.h"
-#include "colvarbias.h"
-#include "colvaratoms.h"
 #include "colvarproxy.h"
-#include "colvarproxy_lammps.h"
-
-#include <sys/types.h>
-#include <sys/stat.h>
-#include <unistd.h>
-
-#include <cerrno>
-#include <cstdio>
-#include <cstring>
-
-#include <iostream>
-#include <sstream>
-#include <string>
 
 #define HASH_FAIL  -1
 
diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h
index c3d9dbb35f..8ed03309a3 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.h
+++ b/src/USER-COLVARS/colvarproxy_lammps.h
@@ -10,33 +10,22 @@
 #ifndef COLVARPROXY_LAMMPS_H
 #define COLVARPROXY_LAMMPS_H
 
-#include "colvarproxy_lammps_version.h"
+#include "colvarproxy_lammps_version.h"  // IWYU pragma: export
+
+#include <mpi.h>
+#include <cstddef>
+#include <string>
+#include <vector>
 
 #include "colvarmodule.h"
 #include "colvarproxy.h"
-#include "colvarvalue.h"
+#include "colvartypes.h"
 
-#include "lammps.h"
-#include "domain.h"
-#include "force.h"
-#include "update.h"
-
-#include <string>
-#include <vector>
-#include <iostream>
-
-/* struct for packed data communication of coordinates and forces. */
-struct commdata {
-  int tag,type;
-  double x,y,z,m,q;
-};
-
-inline std::ostream & operator<< (std::ostream &out, const commdata &cd)
-{
-  out << " (" << cd.tag << "/" << cd.type << ": "
-      << cd.x << ", " << cd.y << ", " << cd.z << ") ";
-  return out;
-}
+#include "random_park.h"
+#include "lammps.h"  // IWYU pragma: keep
+#include "domain.h"  // IWYU pragma: keep
+#include "force.h"   // IWYU pragma: keep
+#include "update.h"  // IWYU pragma: keep
 
 /// \brief Communication between colvars and LAMMPS
 /// (implementation of \link colvarproxy \endlink)
@@ -46,8 +35,8 @@ class colvarproxy_lammps : public colvarproxy {
  protected:
 
   // pointers to LAMMPS class instances
-  class LAMMPS_NS::LAMMPS *_lmp;
-  class LAMMPS_NS::RanPark *_random;
+  LAMMPS_NS::LAMMPS *_lmp;
+  LAMMPS_NS::RanPark *_random;
 
   // state of LAMMPS properties
   double t_target, my_timestep, my_boltzmann, my_angstrom;
diff --git a/src/USER-COLVARS/colvarproxy_lammps_version.h b/src/USER-COLVARS/colvarproxy_lammps_version.h
index 0a4f9fdf4f..d976f40510 100644
--- a/src/USER-COLVARS/colvarproxy_lammps_version.h
+++ b/src/USER-COLVARS/colvarproxy_lammps_version.h
@@ -1,5 +1,5 @@
 #ifndef COLVARPROXY_VERSION
-#define COLVARPROXY_VERSION "2019-04-09"
+#define COLVARPROXY_VERSION "2019-08-01"
 // This file is part of the Collective Variables module (Colvars).
 // The original version of Colvars and its updates are located at:
 // https://github.com/colvars/colvars
diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp
index ff0e8fb334..4a57e59fbd 100644
--- a/src/USER-COLVARS/fix_colvars.cpp
+++ b/src/USER-COLVARS/fix_colvars.cpp
@@ -24,27 +24,29 @@
    Contributing author:  Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
+#include "fix_colvars.h"
+#include <mpi.h>
 #include <cstdlib>
 #include <cstring>
-#include <errno.h>
+#include <iostream>
+#include <string>
+#include <vector>
+#include <memory>
 
-#include "fix_colvars.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "group.h"
+#include "force.h"
 #include "memory.h"
 #include "modify.h"
-#include "random_park.h"
 #include "respa.h"
 #include "universe.h"
 #include "update.h"
 #include "citeme.h"
 
 #include "colvarproxy_lammps.h"
+#include "colvarmodule.h"
 
 static const char colvars_pub[] =
   "fix colvars command:\n\n"
@@ -57,6 +59,19 @@ static const char colvars_pub[] =
   " note =    {doi: 10.1080/00268976.2013.813594}\n"
   "}\n\n";
 
+/* struct for packed data communication of coordinates and forces. */
+struct LAMMPS_NS::commdata {
+  int tag,type;
+  double x,y,z,m,q;
+};
+
+inline std::ostream & operator<< (std::ostream &out, const LAMMPS_NS::commdata &cd)
+{
+  out << " (" << cd.tag << "/" << cd.type << ": "
+      << cd.x << ", " << cd.y << ", " << cd.z << ") ";
+  return out;
+}
+
 /* re-usable integer hash table code with static linkage. */
 
 /** hash table top level data structure */
diff --git a/src/USER-COLVARS/fix_colvars.h b/src/USER-COLVARS/fix_colvars.h
index a0c197fca4..985457e746 100644
--- a/src/USER-COLVARS/fix_colvars.h
+++ b/src/USER-COLVARS/fix_colvars.h
@@ -34,10 +34,9 @@ FixStyle(colvars,FixColvars)
 #define LMP_FIX_COLVARS_H
 
 #include "fix.h"
+#include <mpi.h>
 
-// forward declaration
 class colvarproxy_lammps;
-struct commdata;
 
 namespace LAMMPS_NS {
 
@@ -64,7 +63,7 @@ class FixColvars : public Fix {
   virtual void restart(char *);
 
  protected:
-  class colvarproxy_lammps *proxy; // pointer to the colvars proxy class
+  colvarproxy_lammps *proxy; // pointer to the colvars proxy class
   char *conf_file;     // name of colvars config file
   char *inp_name;      // name/prefix of colvars restart file
   char *out_name;      // prefix string for all output files
diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp
index 858336c9d5..1e37e2de9c 100644
--- a/src/USER-COLVARS/group_ndx.cpp
+++ b/src/USER-COLVARS/group_ndx.cpp
@@ -17,15 +17,13 @@
 ------------------------------------------------------------------------- */
 
 #include "group_ndx.h"
+#include <mpi.h>
+#include <cstdlib>
 #include "atom.h"
 #include "comm.h"
 #include "group.h"
-#include "memory.h"
 #include "error.h"
 
-#include <cstdio>
-#include <cstdlib>
-
 using namespace LAMMPS_NS;
 
 /* ----------------------------------------------------------------------
diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp
index 7b46364f18..a1369df2fb 100644
--- a/src/USER-COLVARS/ndx_group.cpp
+++ b/src/USER-COLVARS/ndx_group.cpp
@@ -17,17 +17,14 @@
 ------------------------------------------------------------------------- */
 
 #include "ndx_group.h"
+#include <mpi.h>
+#include <cstdlib>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "group.h"
-#include "memory.h"
-#include "force.h"
 #include "error.h"
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-
 using namespace LAMMPS_NS;
 #define BUFLEN 4096
 #define DELTA 16384
diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp
index dcafe57ba8..971d9bd380 100644
--- a/src/USER-DIFFRACTION/compute_saed.cpp
+++ b/src/USER-DIFFRACTION/compute_saed.cpp
@@ -15,13 +15,12 @@
    Contributing authors: Shawn Coleman & Douglas Spearot (Arkansas)
 ------------------------------------------------------------------------- */
 
+#include "compute_saed.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstdlib>
-#include <cstdio>
 #include <cstring>
 #include "math_const.h"
-#include "compute_saed.h"
 #include "compute_saed_consts.h"
 #include "atom.h"
 #include "comm.h"
diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp
index d6b7549272..f48951f1ff 100644
--- a/src/USER-DIFFRACTION/compute_xrd.cpp
+++ b/src/USER-DIFFRACTION/compute_xrd.cpp
@@ -16,13 +16,12 @@
    Updated: 06/17/2015-2
 ------------------------------------------------------------------------- */
 
+#include "compute_xrd.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstdlib>
-#include <cstdio>
 #include <cstring>
 #include "math_const.h"
-#include "compute_xrd.h"
 #include "compute_xrd_consts.h"
 #include "atom.h"
 #include "comm.h"
diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
index 4d9af66818..c3a72e494b 100644
--- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp
+++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
@@ -16,17 +16,14 @@
    Incorporating SAED: Shawn Coleman (Arkansas)
 ------------------------------------------------------------------------- */
 
+#include "fix_saed_vtk.h"
 #include <cstdlib>
 #include <cstring>
 #include <cmath>
-#include "fix_saed_vtk.h"
 #include "update.h"
 #include "modify.h"
 #include "compute.h"
 #include "compute_saed.h"
-#include "group.h"
-#include "input.h"
-#include "variable.h"
 #include "memory.h"
 #include "error.h"
 #include "force.h"
diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/USER-DIFFRACTION/fix_saed_vtk.h
index 2fc09c781c..94abbf0194 100644
--- a/src/USER-DIFFRACTION/fix_saed_vtk.h
+++ b/src/USER-DIFFRACTION/fix_saed_vtk.h
@@ -20,7 +20,6 @@ FixStyle(saed/vtk,FixSAEDVTK)
 #ifndef LMP_FIX_SAED_VTK_H
 #define LMP_FIX_SAED_VTK_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp
index de673caec0..d1768d473e 100644
--- a/src/USER-DPD/atom_vec_dpd.cpp
+++ b/src/USER-DPD/atom_vec_dpd.cpp
@@ -15,12 +15,10 @@
    Contributing author: James Larentzos (U.S. Army Research Laboratory)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_dpd.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "memory.h"
diff --git a/src/USER-DPD/compute_dpd.cpp b/src/USER-DPD/compute_dpd.cpp
index 08aa19bcdf..0ef7868164 100644
--- a/src/USER-DPD/compute_dpd.cpp
+++ b/src/USER-DPD/compute_dpd.cpp
@@ -15,13 +15,10 @@
    Contributing author: James Larentzos (U.S. Army Research Laboratory)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "compute_dpd.h"
+#include <mpi.h>
 #include "atom.h"
 #include "update.h"
-#include "force.h"
-#include "domain.h"
-#include "group.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-DPD/compute_dpd_atom.cpp b/src/USER-DPD/compute_dpd_atom.cpp
index 78f842a68f..0fd732f669 100644
--- a/src/USER-DPD/compute_dpd_atom.cpp
+++ b/src/USER-DPD/compute_dpd_atom.cpp
@@ -15,21 +15,15 @@
    Contributing author: James Larentzos (U.S. Army Research Laboratory)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
 #include "compute_dpd_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
-#include "domain.h"
-#include "group.h"
 #include "memory.h"
 #include "error.h"
 #include "comm.h"
 
-#include <vector>
-
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/USER-DPD/fix_dpd_energy.cpp b/src/USER-DPD/fix_dpd_energy.cpp
index 5759a164f5..6ee88ea88a 100644
--- a/src/USER-DPD/fix_dpd_energy.cpp
+++ b/src/USER-DPD/fix_dpd_energy.cpp
@@ -11,14 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
 #include "fix_dpd_energy.h"
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
-#include "modify.h"
 #include "error.h"
 #include "pair_dpd_fdt_energy.h"
 
diff --git a/src/USER-DPD/fix_eos_cv.cpp b/src/USER-DPD/fix_eos_cv.cpp
index 919e6829f3..5b25519a40 100644
--- a/src/USER-DPD/fix_eos_cv.cpp
+++ b/src/USER-DPD/fix_eos_cv.cpp
@@ -15,8 +15,6 @@
    Contributing author: James Larentzos (U.S. Army Research Laboratory)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_eos_cv.h"
 #include "atom.h"
 #include "error.h"
diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp
index 7d701f5fb8..ff9a186c47 100644
--- a/src/USER-DPD/fix_eos_table.cpp
+++ b/src/USER-DPD/fix_eos_table.cpp
@@ -15,9 +15,10 @@
    Contributing author: James Larentzos (U.S. Army Research Laboratory)
 ------------------------------------------------------------------------- */
 
+#include "fix_eos_table.h"
+#include <mpi.h>
 #include <cstdlib>
 #include <cstring>
-#include "fix_eos_table.h"
 #include "atom.h"
 #include "error.h"
 #include "force.h"
diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp
index 779cee0e8b..9f1bd6a3bb 100644
--- a/src/USER-DPD/fix_eos_table_rx.cpp
+++ b/src/USER-DPD/fix_eos_table_rx.cpp
@@ -15,10 +15,11 @@
    Contributing author: James Larentzos (U.S. Army Research Laboratory)
 ------------------------------------------------------------------------- */
 
+#include "fix_eos_table_rx.h"
+#include <mpi.h>
 #include <cstdlib>
 #include <cstring>
 #include <cmath>
-#include "fix_eos_table_rx.h"
 #include "atom.h"
 #include "error.h"
 #include "force.h"
diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp
index cb8349786f..03e8ae49a4 100644
--- a/src/USER-DPD/fix_rx.cpp
+++ b/src/USER-DPD/fix_rx.cpp
@@ -11,12 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
+#include "fix_rx.h"
+#include <mpi.h>
 #include <cstdlib>
 #include <cstring>
 #include <cmath>
 #include <cfloat> // DBL_EPSILON
-#include "fix_rx.h"
 #include "atom.h"
 #include "error.h"
 #include "group.h"
diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp
index 4e133480ad..b0efeb634d 100644
--- a/src/USER-DPD/fix_shardlow.cpp
+++ b/src/USER-DPD/fix_shardlow.cpp
@@ -33,27 +33,25 @@
    135, 204105.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
+#include "fix_shardlow.h"
 #include <cstdlib>
 #include <cstring>
 #include <cmath>
-#include "fix_shardlow.h"
+#include <stdint.h>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
+#include "npair.h"
 #include "memory.h"
 #include "domain.h"
 #include "modify.h"
 #include "pair_dpd_fdt.h"
 #include "pair_dpd_fdt_energy.h"
-#include "pair.h"
 #include "npair_half_bin_newton_ssa.h"
 #include "citeme.h"
 
diff --git a/src/USER-DPD/nbin_ssa.cpp b/src/USER-DPD/nbin_ssa.cpp
index dcd434cb4a..e3fa71aedf 100644
--- a/src/USER-DPD/nbin_ssa.cpp
+++ b/src/USER-DPD/nbin_ssa.cpp
@@ -21,8 +21,6 @@
 #include "update.h"
 #include "group.h"
 #include "domain.h"
-#include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.cpp b/src/USER-DPD/npair_half_bin_newton_ssa.cpp
index ba90ebc465..2139173d47 100644
--- a/src/USER-DPD/npair_half_bin_newton_ssa.cpp
+++ b/src/USER-DPD/npair_half_bin_newton_ssa.cpp
@@ -17,7 +17,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_bin_newton_ssa.h"
-#include "neighbor.h"
 #include "nstencil_ssa.h"
 #include "nbin_ssa.h"
 #include "neigh_list.h"
@@ -25,7 +24,6 @@
 #include "atom_vec.h"
 #include "molecule.h"
 #include "domain.h"
-#include "group.h"
 #include "memory.h"
 #include "my_page.h"
 #include "error.h"
diff --git a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp
index 451381c104..9953fca62c 100644
--- a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp
+++ b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp
@@ -17,8 +17,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_bin_2d_newton_ssa.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp
index cdd3b8856f..4dd3c4a5fe 100644
--- a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp
+++ b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp
@@ -17,8 +17,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_bin_3d_newton_ssa.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp
index 07ef8190f0..1cb9d68d06 100644
--- a/src/USER-DPD/pair_dpd_fdt.cpp
+++ b/src/USER-DPD/pair_dpd_fdt.cpp
@@ -15,23 +15,20 @@
    Contributing author: James Larentzos (U.S. Army Research Laboratory)
 ------------------------------------------------------------------------- */
 
+#include "pair_dpd_fdt.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "update.h"
 #include "fix.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "random_mars.h"
 #include "memory.h"
 #include "modify.h"
-#include "pair_dpd_fdt.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp
index 12e6989c00..22741a055d 100644
--- a/src/USER-DPD/pair_dpd_fdt_energy.cpp
+++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp
@@ -15,23 +15,20 @@
    Contributing author: James Larentzos (U.S. Army Research Laboratory)
 ------------------------------------------------------------------------- */
 
+#include "pair_dpd_fdt_energy.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "update.h"
 #include "fix.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "random_mars.h"
 #include "memory.h"
 #include "modify.h"
-#include "pair_dpd_fdt_energy.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp
index 13521b52b1..5cf2859ae3 100644
--- a/src/USER-DPD/pair_exp6_rx.cpp
+++ b/src/USER-DPD/pair_exp6_rx.cpp
@@ -11,17 +11,16 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "pair_exp6_rx.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 #include <cfloat>
-#include "pair_exp6_rx.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neigh_list.h"
-#include "math_const.h"
 #include "math_special.h"
 #include "memory.h"
 #include "error.h"
@@ -29,7 +28,6 @@
 #include "fix.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace MathSpecial;
 
 #define MAXLINE 1024
diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp
index f2d0d7b1fb..e767f93367 100644
--- a/src/USER-DPD/pair_table_rx.cpp
+++ b/src/USER-DPD/pair_table_rx.cpp
@@ -15,14 +15,12 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_table_rx.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "pair_table_rx.h"
 #include "atom.h"
 #include "force.h"
-#include "comm.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/USER-DRUDE/compute_temp_drude.cpp
index 4830e950d0..a12c248680 100644
--- a/src/USER-DRUDE/compute_temp_drude.cpp
+++ b/src/USER-DRUDE/compute_temp_drude.cpp
@@ -11,19 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
-#include <cstring>
 #include "compute_temp_drude.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
-#include "group.h"
 #include "modify.h"
-#include "fix.h"
+#include "fix_drude.h"
 #include "domain.h"
-#include "lattice.h"
-#include "memory.h"
 #include "error.h"
 #include "comm.h"
 
diff --git a/src/USER-DRUDE/compute_temp_drude.h b/src/USER-DRUDE/compute_temp_drude.h
index 88d767f8b7..530c84ce3d 100644
--- a/src/USER-DRUDE/compute_temp_drude.h
+++ b/src/USER-DRUDE/compute_temp_drude.h
@@ -21,7 +21,6 @@ ComputeStyle(temp/drude,ComputeTempDrude)
 #define LMP_COMPUTE_TEMP_DRUDE_H
 
 #include "compute.h"
-#include "fix_drude.h"
 
 namespace LAMMPS_NS {
 
@@ -37,7 +36,7 @@ class ComputeTempDrude : public Compute {
 
  private:
   int fix_dof;
-  FixDrude * fix_drude;
+  class FixDrude * fix_drude;
   char *id_temp;
   class Compute *temperature;
   bigint dof_core, dof_drude;
diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp
index 7800efe7ff..080408459c 100644
--- a/src/USER-DRUDE/fix_drude.cpp
+++ b/src/USER-DRUDE/fix_drude.cpp
@@ -11,9 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "fix_drude.h"
+#include <mpi.h>
+#include <cstring>
+#include <map>
 #include "atom.h"
 #include "comm.h"
 #include "modify.h"
diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp
index 34742a0683..4128c508d6 100644
--- a/src/USER-DRUDE/fix_drude_transform.cpp
+++ b/src/USER-DRUDE/fix_drude_transform.cpp
@@ -12,15 +12,16 @@
 ------------------------------------------------------------------------- */
 
 /** Fix Drude Transform ******************************************************/
+#include "fix_drude_transform.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include "fix_drude_transform.h"
+#include "fix_drude.h"
 #include "atom.h"
 #include "domain.h"
 #include "comm.h"
 #include "error.h"
 #include "modify.h"
-#include "force.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-DRUDE/fix_drude_transform.h b/src/USER-DRUDE/fix_drude_transform.h
index 41f4e147ed..b74a500c95 100644
--- a/src/USER-DRUDE/fix_drude_transform.h
+++ b/src/USER-DRUDE/fix_drude_transform.h
@@ -22,7 +22,6 @@ FixStyle(drude/transform/inverse,FixDrudeTransform<true>)
 #define LMP_FIX_DRUDE_TRANSFORM_H
 
 #include "fix.h"
-#include "fix_drude.h"
 
 namespace LAMMPS_NS {
 
@@ -42,7 +41,7 @@ class FixDrudeTransform : public Fix {
   void unpack_forward_comm(int n, int first, double *buf);
  protected:
   double * mcoeff;
-  FixDrude * fix_drude;
+  class FixDrude * fix_drude;
 };
 
 }
diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp
index b9d1139f83..d413c31bd7 100644
--- a/src/USER-DRUDE/fix_langevin_drude.cpp
+++ b/src/USER-DRUDE/fix_langevin_drude.cpp
@@ -11,17 +11,17 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "fix_langevin_drude.h"
+#include <mpi.h>
+#include <cstring>
+#include <cmath>
+#include "fix_drude.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
 #include "input.h"
 #include "variable.h"
 #include "random_mars.h"
-#include "group.h"
 #include "update.h"
 #include "modify.h"
 #include "compute.h"
diff --git a/src/USER-DRUDE/fix_langevin_drude.h b/src/USER-DRUDE/fix_langevin_drude.h
index d65440582c..9437883ba3 100644
--- a/src/USER-DRUDE/fix_langevin_drude.h
+++ b/src/USER-DRUDE/fix_langevin_drude.h
@@ -21,7 +21,6 @@ FixStyle(langevin/drude,FixLangevinDrude)
 #define LMP_FIX_LANGEVIN_DRUDE_H
 
 #include "fix.h"
-#include "fix_drude.h"
 
 namespace LAMMPS_NS {
 
@@ -51,7 +50,7 @@ class FixLangevinDrude : public Fix {
   class RanMars *random_core, *random_drude;
   int zero;
   bigint ncore;
-  FixDrude * fix_drude;
+  class FixDrude * fix_drude;
   class Compute *temperature;
   char *id_temp;
 };
diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
index 1ebe4a4c2d..851effd89c 100644
--- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
+++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
@@ -15,20 +15,17 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_thole_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include "fix_drude.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
-#include "update.h"
-#include "integrate.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.h b/src/USER-DRUDE/pair_lj_cut_thole_long.h
index 27a917c737..4c3a883064 100644
--- a/src/USER-DRUDE/pair_lj_cut_thole_long.h
+++ b/src/USER-DRUDE/pair_lj_cut_thole_long.h
@@ -21,7 +21,6 @@ PairStyle(lj/cut/thole/long,PairLJCutTholeLong)
 #define LMP_PAIR_LJ_CUT_THOLE_LONG_H
 
 #include "pair.h"
-#include "fix_drude.h"
 
 namespace LAMMPS_NS {
 
@@ -58,7 +57,7 @@ class PairLJCutTholeLong : public Pair {
   double cut_global;
   double **cut,**scale;
   double **polar,**thole,**ascreen;
-  FixDrude *fix_drude;
+  class FixDrude *fix_drude;
 
   virtual void allocate();
 };
diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp
index 1bb75af825..1f81263e95 100644
--- a/src/USER-DRUDE/pair_thole.cpp
+++ b/src/USER-DRUDE/pair_thole.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_thole.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -24,7 +23,7 @@
 #include "memory.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_store.h"
+#include "fix_drude.h"
 #include "domain.h"
 #include "modify.h"
 
diff --git a/src/USER-DRUDE/pair_thole.h b/src/USER-DRUDE/pair_thole.h
index 2c462b431a..88c00b6d20 100644
--- a/src/USER-DRUDE/pair_thole.h
+++ b/src/USER-DRUDE/pair_thole.h
@@ -21,7 +21,6 @@ PairStyle(thole,PairThole)
 #define LMP_PAIR_THOLE_H
 
 #include "pair.h"
-#include "fix_drude.h"
 
 namespace LAMMPS_NS {
 
@@ -46,7 +45,7 @@ class PairThole : public Pair {
   double cut_global;
   double **cut,**scale;
   double **polar,**thole,**ascreen;
-  FixDrude * fix_drude;
+  class FixDrude * fix_drude;
 
   virtual void allocate();
 };
diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp
index cf4555f02e..552a89c04a 100644
--- a/src/USER-EFF/atom_vec_electron.cpp
+++ b/src/USER-EFF/atom_vec_electron.cpp
@@ -15,15 +15,12 @@
    Contributing author: Andres Jaramillo-Botero (Caltech)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "atom_vec_electron.h"
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
 #include "modify.h"
-#include "force.h"
 #include "fix.h"
 #include "citeme.h"
 #include "memory.h"
diff --git a/src/USER-EFF/compute_ke_atom_eff.cpp b/src/USER-EFF/compute_ke_atom_eff.cpp
index b1b87cd3df..c943366f1b 100644
--- a/src/USER-EFF/compute_ke_atom_eff.cpp
+++ b/src/USER-EFF/compute_ke_atom_eff.cpp
@@ -15,7 +15,6 @@
    Contributing author: Andres Jaramillo-Botero
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include <cstring>
 #include <cstdlib>
 #include "compute_ke_atom_eff.h"
diff --git a/src/USER-EFF/compute_ke_eff.cpp b/src/USER-EFF/compute_ke_eff.cpp
index b4f571cb63..3e277fc66c 100644
--- a/src/USER-EFF/compute_ke_eff.cpp
+++ b/src/USER-EFF/compute_ke_eff.cpp
@@ -16,14 +16,12 @@
 ------------------------------------------------------------------------- */
 
 #include <mpi.h>
-#include <cmath>
 #include <cstdlib>
 #include "compute_ke_eff.h"
 #include "atom.h"
 #include "update.h"
 #include "force.h"
 #include "domain.h"
-#include "group.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp
index 621eff210f..dcf7e86234 100644
--- a/src/USER-EFF/compute_temp_deform_eff.cpp
+++ b/src/USER-EFF/compute_temp_deform_eff.cpp
@@ -16,7 +16,6 @@
 ------------------------------------------------------------------------- */
 
 #include <mpi.h>
-#include <cmath>
 #include <cstring>
 #include <cstdlib>
 #include "compute_temp_deform_eff.h"
diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp
index 956461adf1..e9295ea680 100644
--- a/src/USER-EFF/compute_temp_eff.cpp
+++ b/src/USER-EFF/compute_temp_eff.cpp
@@ -15,11 +15,9 @@
    Contributing author: Andres Jaramillo-Botero (Caltech)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
 #include "compute_temp_eff.h"
+#include <mpi.h>
+#include <cstdlib>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp
index 8cab690367..b27699cde9 100644
--- a/src/USER-EFF/compute_temp_region_eff.cpp
+++ b/src/USER-EFF/compute_temp_region_eff.cpp
@@ -16,14 +16,12 @@
 ------------------------------------------------------------------------- */
 
 #include <mpi.h>
-#include <cmath>
 #include <cstring>
 #include <cstdlib>
 #include "compute_temp_region_eff.h"
 #include "atom.h"
 #include "update.h"
 #include "force.h"
-#include "modify.h"
 #include "domain.h"
 #include "region.h"
 #include "group.h"
diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp
index d362113997..5158d7c681 100644
--- a/src/USER-EFF/fix_langevin_eff.cpp
+++ b/src/USER-EFF/fix_langevin_eff.cpp
@@ -17,19 +17,13 @@
 
 #include <mpi.h>
 #include <cmath>
-#include <cstring>
 #include <cstdlib>
 #include "fix_langevin_eff.h"
-#include "math_extra.h"
 #include "atom.h"
-#include "force.h"
 #include "update.h"
 #include "modify.h"
 #include "compute.h"
 #include "domain.h"
-#include "region.h"
-#include "respa.h"
-#include "comm.h"
 #include "input.h"
 #include "variable.h"
 #include "random_mars.h"
diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp
index 3e0a59612c..034233732e 100644
--- a/src/USER-EFF/fix_nh_eff.cpp
+++ b/src/USER-EFF/fix_nh_eff.cpp
@@ -15,12 +15,10 @@
    Contributing author: Andres Jaramillo-Botero (Caltech)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include <cstdlib>
 #include "fix_nh_eff.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "group.h"
 #include "error.h"
 #include "domain.h"
 
diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp
index 699dd9f949..ea719c91c0 100644
--- a/src/USER-EFF/fix_nve_eff.cpp
+++ b/src/USER-EFF/fix_nve_eff.cpp
@@ -15,8 +15,6 @@
    Contributing author: Andres Jaramillo-Botero (Caltech)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
 #include <cstring>
 #include <cstdlib>
 #include "fix_nve_eff.h"
diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp
index 9e23ee023b..8516accd31 100644
--- a/src/USER-EFF/fix_nvt_eff.cpp
+++ b/src/USER-EFF/fix_nvt_eff.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include <cstring>
-#include <cmath>
 #include "fix_nvt_eff.h"
 #include "group.h"
 #include "modify.h"
diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp
index ed2274dcf9..0ebbf04d64 100644
--- a/src/USER-EFF/fix_nvt_sllod_eff.cpp
+++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp
@@ -12,6 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include <cmath>
+#include <cstring>
 #include <cstdlib>
 #include "fix_nvt_sllod_eff.h"
 #include "math_extra.h"
diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp
index 37f45b3c28..4a8f4b0372 100644
--- a/src/USER-EFF/fix_temp_rescale_eff.cpp
+++ b/src/USER-EFF/fix_temp_rescale_eff.cpp
@@ -23,8 +23,6 @@
 #include "force.h"
 #include "group.h"
 #include "update.h"
-#include "domain.h"
-#include "region.h"
 #include "comm.h"
 #include "modify.h"
 #include "compute.h"
diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp
index f566922ef7..a4c0557620 100644
--- a/src/USER-EFF/pair_eff_cut.cpp
+++ b/src/USER-EFF/pair_eff_cut.cpp
@@ -15,8 +15,8 @@
    Contributing author: Andres Jaramillo-Botero
 ------------------------------------------------------------------------- */
 
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 #include "pair_eff_cut.h"
@@ -31,7 +31,6 @@
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
-#include "atom_vec_electron.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-FEP/compute_fep.cpp b/src/USER-FEP/compute_fep.cpp
index dc0b71e71b..1853828db3 100644
--- a/src/USER-FEP/compute_fep.cpp
+++ b/src/USER-FEP/compute_fep.cpp
@@ -15,7 +15,7 @@
    Contributing author: Agilio Padua (Univ Blaise Pascal & CNRS)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
+#include "compute_fep.h"
 #include <cstring>
 #include <cmath>
 #include <mpi.h>
@@ -34,7 +34,6 @@
 #include "timer.h"
 #include "memory.h"
 #include "error.h"
-#include "compute_fep.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp
index 7304bc4ef6..46cf32cf0b 100644
--- a/src/USER-FEP/fix_adapt_fep.cpp
+++ b/src/USER-FEP/fix_adapt_fep.cpp
@@ -15,10 +15,8 @@
    Charges by type and after option: Agilio Padua (Univ Blaise Pascal & CNRS)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
 #include "fix_adapt_fep.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "group.h"
diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp
index 86a6d02819..a4ff3ca846 100644
--- a/src/USER-FEP/pair_coul_cut_soft.cpp
+++ b/src/USER-FEP/pair_coul_cut_soft.cpp
@@ -15,11 +15,10 @@
    Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_cut_soft.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp
index 9d3ffc0da1..c0030f8935 100644
--- a/src/USER-FEP/pair_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_coul_long_soft.cpp
@@ -16,19 +16,16 @@
    Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_long_soft.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "update.h"
-#include "integrate.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
index ac6f1e6384..4c3be6addb 100644
--- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
@@ -16,17 +16,15 @@
    Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_charmm_coul_long_soft.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp
index ae79515488..bbe67e4ff3 100644
--- a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp
+++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_class2_coul_cut_soft.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp
index 275486d1e2..a3e0f732a2 100644
--- a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_class2_coul_long_soft.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-FEP/pair_lj_class2_soft.cpp b/src/USER-FEP/pair_lj_class2_soft.cpp
index d22cd53883..d98a5db5f3 100644
--- a/src/USER-FEP/pair_lj_class2_soft.cpp
+++ b/src/USER-FEP/pair_lj_class2_soft.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_class2_soft.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
index 35c9162dbc..38fcb6fc07 100644
--- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
@@ -15,11 +15,10 @@
    Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_coul_cut_soft.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
index 79253d2b9c..740daabf62 100644
--- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
@@ -16,17 +16,15 @@
    Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_coul_long_soft.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp
index 4192d6546b..5e9a77877e 100644
--- a/src/USER-FEP/pair_lj_cut_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_soft.cpp
@@ -16,11 +16,10 @@
    Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_soft.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -28,7 +27,6 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "math_const.h"
 #include "memory.h"
diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
index 8ac28f9fa9..d4f6dcb910 100644
--- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
@@ -17,23 +17,18 @@
    Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_tip4p_long_soft.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "angle.h"
 #include "atom.h"
 #include "bond.h"
 #include "comm.h"
 #include "domain.h"
 #include "force.h"
-#include "kspace.h"
-#include "update.h"
-#include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp
index 21f616a082..2803e7df49 100644
--- a/src/USER-FEP/pair_morse_soft.cpp
+++ b/src/USER-FEP/pair_morse_soft.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_morse_soft.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp
index 9b6a6841fe..9cea5b54c5 100644
--- a/src/USER-FEP/pair_tip4p_long_soft.cpp
+++ b/src/USER-FEP/pair_tip4p_long_soft.cpp
@@ -17,23 +17,18 @@
    Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_tip4p_long_soft.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "angle.h"
 #include "atom.h"
 #include "bond.h"
 #include "comm.h"
 #include "domain.h"
 #include "force.h"
-#include "kspace.h"
-#include "update.h"
-#include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-INTEL/TEST/run_benchmarks.sh b/src/USER-INTEL/TEST/run_benchmarks.sh
index 10bd79e0d1..e26c633b68 100755
--- a/src/USER-INTEL/TEST/run_benchmarks.sh
+++ b/src/USER-INTEL/TEST/run_benchmarks.sh
@@ -40,7 +40,7 @@ export LMP_THREAD_LIST="2"     # -- For 2 threads per core w/ HT enabled
 # End settings for your system
 #########################################################################
 
-export WORKLOADS="lj rhodo rhodo_lrt lc sw water eam"
+export WORKLOADS="lj rhodo lc sw water eam airebo dpd tersoff"
 export LMP_ARGS="-pk intel 0 -sf intel -screen none -v d 1"
 export RLMP_ARGS="-pk intel 0 lrt yes -sf intel -screen none -v d 1"
 
@@ -51,7 +51,7 @@ export LOG_DIR=$LOG_DIR_HOST"_"$LOG_DIR_HEADER"_"$DATE_STRING
 mkdir $LOG_DIR
 
 export I_MPI_PIN_DOMAIN=core
-export I_MPI_FABRICS=shm
+#export I_MPI_FABRICS=shm
 export KMP_BLOCKTIME=0
 
 echo -n "Creating restart file...."
@@ -59,13 +59,12 @@ $MPI -np $LMP_CORES $LMP_BIN -in in.lc_generate_restart -log none $LMP_ARGS
 echo "Done."
 for threads in $LMP_THREAD_LIST
 do
-  export OMP_NUM_THREADS=$threads
   for workload in $WORKLOADS
   do
     export LOGFILE=$LOG_DIR/$workload.$LMP_CORES"c"$threads"t".log
     echo "Running $LOGFILE"
     cmd="$MPI -np $LMP_CORES $LMP_BIN -in in.intel.$workload -log $LOGFILE $LMP_ARGS";
-    rthreads=$threads
+    export OMP_NUM_THREADS=$threads
     unset KMP_AFFINITY
     $cmd
 
diff --git a/src/USER-INTEL/angle_charmm_intel.h b/src/USER-INTEL/angle_charmm_intel.h
index 5d173ee6a9..155ecfaff9 100644
--- a/src/USER-INTEL/angle_charmm_intel.h
+++ b/src/USER-INTEL/angle_charmm_intel.h
@@ -24,7 +24,6 @@ AngleStyle(charmm/intel,AngleCharmmIntel)
 #ifndef LMP_ANGLE_CHARMM_INTEL_H
 #define LMP_ANGLE_CHARMM_INTEL_H
 
-#include <cstdio>
 #include "angle_charmm.h"
 #include "fix_intel.h"
 
diff --git a/src/USER-INTEL/angle_harmonic_intel.h b/src/USER-INTEL/angle_harmonic_intel.h
index e7768542a1..c00292f7ce 100644
--- a/src/USER-INTEL/angle_harmonic_intel.h
+++ b/src/USER-INTEL/angle_harmonic_intel.h
@@ -24,7 +24,6 @@ AngleStyle(harmonic/intel,AngleHarmonicIntel)
 #ifndef LMP_ANGLE_HARMONIC_INTEL_H
 #define LMP_ANGLE_HARMONIC_INTEL_H
 
-#include <cstdio>
 #include "angle_harmonic.h"
 #include "fix_intel.h"
 
diff --git a/src/USER-INTEL/bond_fene_intel.h b/src/USER-INTEL/bond_fene_intel.h
index afe3b85470..58fcdb8669 100644
--- a/src/USER-INTEL/bond_fene_intel.h
+++ b/src/USER-INTEL/bond_fene_intel.h
@@ -24,7 +24,6 @@ BondStyle(fene/intel,BondFENEIntel)
 #ifndef LMP_BOND_FENE_INTEL_H
 #define LMP_BOND_FENE_INTEL_H
 
-#include <cstdio>
 #include "bond_fene.h"
 #include "fix_intel.h"
 
diff --git a/src/USER-INTEL/bond_harmonic_intel.h b/src/USER-INTEL/bond_harmonic_intel.h
index b86a560d6e..3c1d050a3b 100644
--- a/src/USER-INTEL/bond_harmonic_intel.h
+++ b/src/USER-INTEL/bond_harmonic_intel.h
@@ -24,7 +24,6 @@ BondStyle(harmonic/intel,BondHarmonicIntel)
 #ifndef LMP_BOND_HARMONIC_INTEL_H
 #define LMP_BOND_HARMONIC_INTEL_H
 
-#include <cstdio>
 #include "bond_harmonic.h"
 #include "fix_intel.h"
 
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index bdc47827ab..83a22f0562 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -352,15 +352,15 @@ void FixIntel::init()
   if (_offload_balance != 0.0) off_mode = 1;
   if (_precision_mode == PREC_MODE_SINGLE) {
     _single_buffers->zero_ev();
-    _single_buffers->grow_ncache(off_mode,_nthreads);
+    _single_buffers->grow_ncache(off_mode, comm->nthreads);
     _single_buffers->free_list_ptrs();
   } else if (_precision_mode == PREC_MODE_MIXED) {
     _mixed_buffers->zero_ev();
-    _mixed_buffers->grow_ncache(off_mode,_nthreads);
+    _mixed_buffers->grow_ncache(off_mode, comm->nthreads);
     _mixed_buffers->free_list_ptrs();
   } else {
     _double_buffers->zero_ev();
-    _double_buffers->grow_ncache(off_mode,_nthreads);
+    _double_buffers->grow_ncache(off_mode, comm->nthreads);
     _double_buffers->free_list_ptrs();
   }
 
diff --git a/src/USER-INTEL/improper_cvff_intel.h b/src/USER-INTEL/improper_cvff_intel.h
index e815fa75c9..812b49d50c 100644
--- a/src/USER-INTEL/improper_cvff_intel.h
+++ b/src/USER-INTEL/improper_cvff_intel.h
@@ -24,7 +24,6 @@ ImproperStyle(cvff/intel,ImproperCvffIntel)
 #ifndef LMP_IMPROPER_CVFF_INTEL_H
 #define LMP_IMPROPER_CVFF_INTEL_H
 
-#include <cstdio>
 #include "improper_cvff.h"
 #include "fix_intel.h"
 
diff --git a/src/USER-INTEL/improper_harmonic_intel.h b/src/USER-INTEL/improper_harmonic_intel.h
index ce38e8fc31..6d7c829961 100644
--- a/src/USER-INTEL/improper_harmonic_intel.h
+++ b/src/USER-INTEL/improper_harmonic_intel.h
@@ -24,7 +24,6 @@ ImproperStyle(harmonic/intel,ImproperHarmonicIntel)
 #ifndef LMP_IMPROPER_HARMONIC_INTEL_H
 #define LMP_IMPROPER_HARMONIC_INTEL_H
 
-#include <cstdio>
 #include "improper_harmonic.h"
 #include "fix_intel.h"
 
diff --git a/src/USER-INTEL/intel_intrinsics_airebo.h b/src/USER-INTEL/intel_intrinsics_airebo.h
index 2b55b41ad1..cadf80bbe8 100644
--- a/src/USER-INTEL/intel_intrinsics_airebo.h
+++ b/src/USER-INTEL/intel_intrinsics_airebo.h
@@ -2223,7 +2223,9 @@ public:
   }
 
   VEC_INLINE static ivec unpackloepi32(const fvec &a) {
-    return reinterpret_cast<const int*>(&a.val_)[0];
+    union { int i; flt_t f; } atype;
+    atype.f = a.val_;
+    return ivec(atype.i);
   }
 
   VEC_INLINE static fvec mask_sincos(
diff --git a/src/USER-INTEL/intel_simd.h b/src/USER-INTEL/intel_simd.h
index 75fc9828b9..9022f439c4 100644
--- a/src/USER-INTEL/intel_simd.h
+++ b/src/USER-INTEL/intel_simd.h
@@ -29,7 +29,6 @@ authors for more details.
 #ifndef INTEL_SIMD_H
 #define INTEL_SIMD_H
 
-#include <cstdio>
 #include "intel_preprocess.h"
 #include "immintrin.h"
 
diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp
index 9d2629ef1c..32d7e74cbc 100644
--- a/src/USER-INTEL/pair_eam_intel.cpp
+++ b/src/USER-INTEL/pair_eam_intel.cpp
@@ -451,7 +451,6 @@ void PairEAMIntel::eval(const int offload, const int vflag,
 
       if (tid == 0)
         comm->forward_comm_pair(this);
-      if (NEWTON_PAIR) memset(f + minlocal, 0, f_stride * sizeof(FORCE_T));
 
       #if defined(_OPENMP)
       #pragma omp barrier
diff --git a/src/USER-INTEL/pair_eam_intel.h b/src/USER-INTEL/pair_eam_intel.h
index 83b1fbf6a1..a9590f6b3d 100644
--- a/src/USER-INTEL/pair_eam_intel.h
+++ b/src/USER-INTEL/pair_eam_intel.h
@@ -20,7 +20,6 @@ PairStyle(eam/intel,PairEAMIntel)
 #ifndef LMP_PAIR_EAM_INTEL_H
 #define LMP_PAIR_EAM_INTEL_H
 
-#include <cstdio>
 #include "pair_eam.h"
 #include "fix_intel.h"
 
diff --git a/src/USER-INTEL/verlet_lrt_intel.cpp b/src/USER-INTEL/verlet_lrt_intel.cpp
index 2b28eea3a2..a3c05c46bc 100644
--- a/src/USER-INTEL/verlet_lrt_intel.cpp
+++ b/src/USER-INTEL/verlet_lrt_intel.cpp
@@ -102,18 +102,20 @@ void VerletLRTIntel::setup(int flag)
   }
 
   #if defined(_LMP_INTEL_LRT_PTHREAD)
+  #if defined(__linux)
   if (comm->me == 0) {
     cpu_set_t cpuset;
     sched_getaffinity(0, sizeof(cpuset), &cpuset);
     int my_cpu_count = CPU_COUNT(&cpuset);
     if (my_cpu_count < comm->nthreads + 1) {
       char str[128];
-      sprintf(str,"Using %d threads per MPI, but only %d core(s) allocated"
-                  " per MPI",
+      sprintf(str,"Using %d threads per MPI rank, but only %d core(s)"
+                  " allocated for each MPI rank",
               comm->nthreads + 1, my_cpu_count);
       error->warning(FLERR, str);
     }
   }
+  #endif
 
   _kspace_ready = 0;
   _kspace_done = 0;
diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp
index 31c54aee76..8ad3dbe33e 100644
--- a/src/USER-LB/fix_lb_fluid.cpp
+++ b/src/USER-LB/fix_lb_fluid.cpp
@@ -20,15 +20,14 @@
 #include <cmath>
 #include <mpi.h>
 #include <cstdlib>
-#include <cstdio>
 #include <cstring>
+#include <algorithm>
+#include <utility>
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
 #include "domain.h"
 #include "atom.h"
-#include <iostream>
-#include <iomanip>
 #include "group.h"
 #include "random_mars.h"
 #include "update.h"
diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp
index df17561380..10fffed018 100644
--- a/src/USER-LB/fix_lb_momentum.cpp
+++ b/src/USER-LB/fix_lb_momentum.cpp
@@ -18,16 +18,15 @@
    Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
 ------------------------------------------------------------------------- */
 
+#include "fix_lb_momentum.h"
+#include <mpi.h>
 #include <cstdlib>
 #include <cstring>
-#include "fix_lb_momentum.h"
 #include "atom.h"
-#include "domain.h"
 #include "group.h"
 #include "error.h"
 #include "fix_lb_fluid.h"
 #include "modify.h"
-#include "comm.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp
index ce6ca0c9a1..d61692419a 100644
--- a/src/USER-LB/fix_lb_pc.cpp
+++ b/src/USER-LB/fix_lb_pc.cpp
@@ -15,17 +15,14 @@
    Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_lb_pc.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
 #include "memory.h"
-#include "comm.h"
 #include "domain.h"
 #include "fix_lb_fluid.h"
 #include "modify.h"
diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
index 83dc751631..af1b01043d 100644
--- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
+++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
@@ -16,21 +16,18 @@
    Based on fix_rigid (version from 2008).
 ------------------------------------------------------------------------- */
 
+#include "fix_lb_rigid_pc_sphere.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "fix_lb_rigid_pc_sphere.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "domain.h"
 #include "update.h"
-#include "respa.h"
 #include "modify.h"
 #include "group.h"
 #include "comm.h"
 #include "force.h"
-#include "output.h"
 #include "memory.h"
 #include "error.h"
 #include "fix_lb_fluid.h"
diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/USER-LB/fix_lb_viscous.cpp
index afe23477be..59fddebd67 100644
--- a/src/USER-LB/fix_lb_viscous.cpp
+++ b/src/USER-LB/fix_lb_viscous.cpp
@@ -15,10 +15,8 @@
    Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_lb_viscous.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "respa.h"
diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp
index 00293bfec7..74a9a1833f 100644
--- a/src/USER-MANIFOLD/fix_manifoldforce.cpp
+++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
+#include "fix_manifoldforce.h"  // For stuff
+#include <mpi.h>
 #include <cstring>
-#include <cstdlib>
 #include "atom.h"
 #include "update.h"
 #include "respa.h"
@@ -21,7 +21,6 @@
 #include "force.h"
 
 #include "manifold.h"
-#include "fix_manifoldforce.h"  // For stuff
 #include "manifold_factory.h"   // For constructing manifold
 
 
diff --git a/src/USER-MANIFOLD/fix_manifoldforce.h b/src/USER-MANIFOLD/fix_manifoldforce.h
index 527bee3f86..1d5afc7afc 100644
--- a/src/USER-MANIFOLD/fix_manifoldforce.h
+++ b/src/USER-MANIFOLD/fix_manifoldforce.h
@@ -43,9 +43,9 @@ FixStyle(manifoldforce,FixManifoldForce)
 #define LMP_FIX_MANIFOLDFORCE_H
 
 #include "fix.h"
-#include "manifold.h"
 
 namespace LAMMPS_NS {
+namespace user_manifold { class manifold; }
 
 class FixManifoldForce : public Fix {
  public:
diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
index de134e32ed..7f8d9d5675 100644
--- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
@@ -32,24 +32,18 @@
 ------------------------------------------------------------------------- */
 
 
-#include <cstdio>
-#include <cstdlib>
+#include "fix_nve_manifold_rattle.h"
+#include <mpi.h>
 #include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
-#include "group.h"
-#include <cmath>
 #include "input.h"
 #include "variable.h"
 #include "citeme.h"
-#include "memory.h"
 #include "comm.h"
 
-
-#include "fix_nve_manifold_rattle.h"
 #include "manifold_factory.h"
 #include "manifold.h"
 
diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h
index 2bc821ab04..581ecf36d3 100644
--- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h
+++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h
@@ -42,12 +42,10 @@ FixStyle(nve/manifold/rattle,FixNVEManifoldRattle)
 #define LMP_FIX_NVE_MANIFOLD_RATTLE_H
 
 #include "fix.h"
-#include "manifold.h"
-
 
 namespace LAMMPS_NS {
 
-// namespace user_manifold {
+namespace user_manifold { class manifold; }
 
   class FixNVEManifoldRattle : public Fix {
    public:
@@ -98,9 +96,7 @@ namespace LAMMPS_NS {
 
     user_manifold::manifold *ptr_m;
 
-
     void print_stats( const char * );
-
     int was_var( const char * );
 
     virtual void update_var_params();
diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
index a4eed66336..2789f8738a 100644
--- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
@@ -32,25 +32,18 @@
 ------------------------------------------------------------------------- */
 
 
-#include <cstdio>
-#include <cstdlib>
+#include "fix_nvt_manifold_rattle.h"
 #include <cstring>
 #include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
 #include "group.h"
-#include "input.h"
-#include "variable.h"
 #include "citeme.h"
-#include "memory.h"
-#include "comm.h"
 #include "modify.h"
 #include "compute.h"
 
-#include "fix_nvt_manifold_rattle.h"
 #include "manifold.h"
 
 
diff --git a/src/USER-MANIFOLD/manifold_factory.h b/src/USER-MANIFOLD/manifold_factory.h
index cc3e1245bf..ac2aee8a26 100644
--- a/src/USER-MANIFOLD/manifold_factory.h
+++ b/src/USER-MANIFOLD/manifold_factory.h
@@ -35,8 +35,7 @@
 #ifndef LMP_MANIFOLD_FACTORY_H
 #define LMP_MANIFOLD_FACTORY_H
 
-
-#include "manifold.h"
+#include <cstddef>
 #include <cstring>
 
 /*
@@ -79,14 +78,16 @@ static FILE *screen = fopen("/dev/stdout","w");
 #define FLERR __FILE__,__LINE__    // Equivalent to definition in pointers.h
 #endif // USE_PHONY_LAMMPS
 
-
-
 /* Here the actual implementation of LAMMPS-related functions begins. */
 
 namespace LAMMPS_NS {
+class LAMMPS;
 
 namespace user_manifold {
 
+// forward declaration
+class manifold;
+
   // Templated, so needs to be in header.
   template <typename m_type>
   void make_manifold_if( manifold **man_ptr, const char *name,
@@ -103,8 +104,6 @@ namespace user_manifold {
                             int , char ** );
 
 } // namespace user_manifold
-
 } // namespace LAMMPS_NS
 
-
 #endif // LMP_MANIFOLD_FACTORY_H
diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp
index 530e0a876d..e4ef039832 100644
--- a/src/USER-MANIFOLD/manifold_thylakoid.cpp
+++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp
@@ -1,6 +1,6 @@
 #include "manifold_thylakoid.h"
 #include <cmath>
-
+#include "manifold_thylakoid_shared.h"
 #include "comm.h"
 #include "domain.h" // For some checks regarding the simulation box.
 #include "error.h"
diff --git a/src/USER-MANIFOLD/manifold_thylakoid.h b/src/USER-MANIFOLD/manifold_thylakoid.h
index 5e5d3b9c41..35ad4dfd9c 100644
--- a/src/USER-MANIFOLD/manifold_thylakoid.h
+++ b/src/USER-MANIFOLD/manifold_thylakoid.h
@@ -3,14 +3,11 @@
 
 #include "manifold.h"
 #include <vector>
-#include <cstdio>
-
-#include "manifold_thylakoid_shared.h"
 
 namespace LAMMPS_NS {
 
 namespace user_manifold {
-
+  struct thyla_part;
 
   class manifold_thylakoid : public manifold {
    public:
diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h
index ff9027dfb3..4e5b298ffb 100644
--- a/src/USER-MEAMC/meam.h
+++ b/src/USER-MEAMC/meam.h
@@ -1,13 +1,12 @@
 #ifndef LMP_MEAM_H
 #define LMP_MEAM_H
 
-#include "memory.h"
 #include <cmath>
-#include <cstdlib>
 
 #define maxelt 5
 
 namespace LAMMPS_NS {
+class Memory;
 
 typedef enum { FCC, BCC, HCP, DIM, DIA, B1, C11, L12, B2 } lattice_t;
 
@@ -235,21 +234,6 @@ static inline bool iszero(const double f) {
   return fabs(f) < 1e-20;
 }
 
-template <typename TYPE, size_t maxi, size_t maxj>
-static inline void setall2d(TYPE (&arr)[maxi][maxj], const TYPE v) {
-  for (size_t i = 0; i < maxi; i++)
-    for (size_t j = 0; j < maxj; j++)
-      arr[i][j] = v;
-}
-
-template <typename TYPE, size_t maxi, size_t maxj, size_t maxk>
-static inline void setall3d(TYPE (&arr)[maxi][maxj][maxk], const TYPE v) {
-  for (size_t i = 0; i < maxi; i++)
-    for (size_t j = 0; j < maxj; j++)
-      for (size_t k = 0; k < maxk; k++)
-        arr[i][j][k] = v;
-}
-
 // Helper functions
 
 static inline double fdiv_zero(const double n, const double d) {
diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp
index c55b1b45c4..867106df88 100644
--- a/src/USER-MEAMC/meam_dens_final.cpp
+++ b/src/USER-MEAMC/meam_dens_final.cpp
@@ -1,5 +1,4 @@
 #include "meam.h"
-#include "math_special.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp
index 3bb9328142..155941422c 100644
--- a/src/USER-MEAMC/meam_dens_init.cpp
+++ b/src/USER-MEAMC/meam_dens_init.cpp
@@ -1,4 +1,6 @@
 #include "meam.h"
+#include <cmath>
+#include "memory.h"
 #include "math_special.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp
index 06fbb57adb..09aad90111 100644
--- a/src/USER-MEAMC/meam_force.cpp
+++ b/src/USER-MEAMC/meam_force.cpp
@@ -1,6 +1,7 @@
 #include "meam.h"
-#include "math_special.h"
+#include <cmath>
 #include <algorithm>
+#include "math_special.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp
index b099ead8d5..74e8af1cde 100644
--- a/src/USER-MEAMC/meam_impl.cpp
+++ b/src/USER-MEAMC/meam_impl.cpp
@@ -16,6 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "meam.h"
+#include <cstddef>
 #include "memory.h"
 
 using namespace LAMMPS_NS;
@@ -43,7 +44,7 @@ MEAM::MEAM(Memory* mem)
       rho_ref_meam[i] = ibar_meam[i] = ielt_meam[i] = 0.0;
     for (int j = 0; j < maxelt; j++) {
       lattce_meam[i][j] = FCC;
-      Ec_meam[i][j] = re_meam[i][j] = alpha_meam[i][j] = delta_meam[i][j] = Ec_meam[i][j] = ebound_meam[i][j] = attrac_meam[i][j] = repuls_meam[i][j] = 0.0;
+      Ec_meam[i][j] = re_meam[i][j] = alpha_meam[i][j] = delta_meam[i][j] = ebound_meam[i][j] = attrac_meam[i][j] = repuls_meam[i][j] = 0.0;
       nn2_meam[i][j] = zbl_meam[i][j] = eltind[i][j] = 0;
     }
   }
diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp
index 2a762d1204..7000eac6ae 100644
--- a/src/USER-MEAMC/meam_setup_done.cpp
+++ b/src/USER-MEAMC/meam_setup_done.cpp
@@ -1,6 +1,10 @@
 #include "meam.h"
-#include "math_special.h"
+#include <cmath>
+#include <cstddef>
 #include <algorithm>
+#include "math_special.h"
+#include "memory.h"
+
 using namespace LAMMPS_NS;
 
 void
diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp
index 503ee65496..b66aafa06c 100644
--- a/src/USER-MEAMC/meam_setup_global.cpp
+++ b/src/USER-MEAMC/meam_setup_global.cpp
@@ -2,6 +2,21 @@
 #include <cmath>
 using namespace LAMMPS_NS;
 
+template <typename TYPE, int maxi, int maxj>
+static inline void setall2d(TYPE (&arr)[maxi][maxj], const TYPE v) {
+  for (int i = 0; i < maxi; i++)
+    for (int j = 0; j < maxj; j++)
+      arr[i][j] = v;
+}
+
+template <typename TYPE, int maxi, int maxj, int maxk>
+static inline void setall3d(TYPE (&arr)[maxi][maxj][maxk], const TYPE v) {
+  for (int i = 0; i < maxi; i++)
+    for (int j = 0; j < maxj; j++)
+      for (int k = 0; k < maxk; k++)
+        arr[i][j][k] = v;
+}
+
 void
 MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* /*atwt*/, double* alpha,
                         double* b0, double* b1, double* b2, double* b3, double* alat, double* esub,
@@ -56,7 +71,7 @@ MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, doub
   setall2d(this->repuls_meam, 0.0);
   setall3d(this->Cmax_meam, 2.8);
   setall3d(this->Cmin_meam, 2.0);
-  setall2d(this->ebound_meam, pow(2.8, 2) / (4.0 * (2.8 - 1.0)));
+  setall2d(this->ebound_meam, (2.8*2.8) / (4.0 * (2.8 - 1.0)));
   setall2d(this->delta_meam, 0.0);
   setall2d(this->nn2_meam, 0);
   setall2d(this->zbl_meam, 1);
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index 7c96fadb44..a9034a1af3 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -15,16 +15,14 @@
    Contributing author: Greg Wagner (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
+#include "pair_meamc.h"
+#include <mpi.h>
 #include <cstdlib>
 #include <cstring>
 #include "meam.h"
-#include "pair_meamc.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
-#include "memory.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h
index a006e70bdb..31dd8ba022 100644
--- a/src/USER-MEAMC/pair_meamc.h
+++ b/src/USER-MEAMC/pair_meamc.h
@@ -24,7 +24,6 @@ PairStyle(meam,PairMEAMC)
 #include "pair.h"
 
 namespace LAMMPS_NS {
-class MEAM;
 
 class PairMEAMC : public Pair {
  public:
diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESO/atom_vec_edpd.cpp
index eee8ae25b0..edc7a34331 100644
--- a/src/USER-MESO/atom_vec_edpd.cpp
+++ b/src/USER-MESO/atom_vec_edpd.cpp
@@ -10,13 +10,11 @@
 
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
-#include <cstring>
-#include <cstdlib>
 #include "atom_vec_edpd.h"
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "update.h"
diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp
index fd3c01f0c6..4c9db36645 100644
--- a/src/USER-MESO/atom_vec_mdpd.cpp
+++ b/src/USER-MESO/atom_vec_mdpd.cpp
@@ -11,13 +11,11 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "atom_vec_mdpd.h"
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "update.h"
diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp
index f91731f8ac..74ac47066b 100644
--- a/src/USER-MESO/atom_vec_tdpd.cpp
+++ b/src/USER-MESO/atom_vec_tdpd.cpp
@@ -11,19 +11,16 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "atom_vec_tdpd.h"
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "force.h"
 #include "domain.h"
 #include "modify.h"
 #include "fix.h"
 #include "update.h"
 #include "memory.h"
 #include "error.h"
-#include "input.h"
 #include "utils.h"
 
 using namespace LAMMPS_NS;
@@ -66,7 +63,7 @@ void AtomVecTDPD::process_args(int narg, char **arg)
 {
   if (narg < 1) error->all(FLERR,"Invalid atom_style tdpd command");
 
-  atom->cc_species = force->inumeric(FLERR,arg[0]);
+  atom->cc_species = utils::inumeric(FLERR,arg[0],false,lmp);
   cc_species = atom->cc_species;
 
   // reset sizes that depend on cc_species
@@ -802,7 +799,7 @@ void AtomVecTDPD::data_atom(double *coord, imageint imagetmp, char **values)
   x[nlocal][2] = coord[2];
 
   for(int k = 0; k < cc_species; k++)
-    cc[nlocal][k] = atof( values[5+k] );
+    cc[nlocal][k] = utils::numeric(FLERR,values[5+k],true,lmp);
 
   image[nlocal] = imagetmp;
 
diff --git a/src/USER-MESO/compute_edpd_temp_atom.cpp b/src/USER-MESO/compute_edpd_temp_atom.cpp
index 119e0079d1..9eb6e9752b 100644
--- a/src/USER-MESO/compute_edpd_temp_atom.cpp
+++ b/src/USER-MESO/compute_edpd_temp_atom.cpp
@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_edpd_temp_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp
index 24bef2b1f7..e62d9a8a79 100644
--- a/src/USER-MESO/fix_edpd_source.cpp
+++ b/src/USER-MESO/fix_edpd_source.cpp
@@ -11,17 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_edpd_source.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "comm.h"
-#include "update.h"
-#include "modify.h"
-#include "domain.h"
-#include "lattice.h"
-#include "input.h"
-#include "variable.h"
 #include "error.h"
 #include "force.h"
 
diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESO/fix_mvv_dpd.cpp
index f663165f78..116bbf506a 100644
--- a/src/USER-MESO/fix_mvv_dpd.cpp
+++ b/src/USER-MESO/fix_mvv_dpd.cpp
@@ -20,13 +20,11 @@
    Email: zhen_li@brown.edu
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
 #include "fix_mvv_dpd.h"
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESO/fix_mvv_edpd.cpp
index 8719d0d262..bd9cd9cc2a 100644
--- a/src/USER-MESO/fix_mvv_edpd.cpp
+++ b/src/USER-MESO/fix_mvv_edpd.cpp
@@ -29,13 +29,11 @@
    Communications, 2015, 51: 11038-11040.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
 #include "fix_mvv_edpd.h"
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESO/fix_mvv_tdpd.cpp
index 24b1bbcf48..b7fe37d7ee 100644
--- a/src/USER-MESO/fix_mvv_tdpd.cpp
+++ b/src/USER-MESO/fix_mvv_tdpd.cpp
@@ -25,13 +25,11 @@
    -reaction problems". The Journal of Chemical Physics, 2015, 143: 014101.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
 #include "fix_mvv_tdpd.h"
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESO/fix_tdpd_source.cpp
index 89e8005b43..990f6a5b78 100644
--- a/src/USER-MESO/fix_tdpd_source.cpp
+++ b/src/USER-MESO/fix_tdpd_source.cpp
@@ -11,17 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_tdpd_source.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "comm.h"
-#include "update.h"
-#include "modify.h"
-#include "domain.h"
-#include "lattice.h"
-#include "input.h"
-#include "variable.h"
 #include "error.h"
 #include "force.h"
 
diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp
index e428b02822..f72b6d6b93 100644
--- a/src/USER-MESO/pair_edpd.cpp
+++ b/src/USER-MESO/pair_edpd.cpp
@@ -16,14 +16,12 @@
    Email: zhen_li@brown.edu
 ------------------------------------------------------------------------- */
 
+#include "pair_edpd.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include <ctime>
 #include <cstring>
-#include "pair_edpd.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESO/pair_mdpd.cpp
index 4102499d46..56adad26ce 100644
--- a/src/USER-MESO/pair_mdpd.cpp
+++ b/src/USER-MESO/pair_mdpd.cpp
@@ -16,13 +16,11 @@
    Email: zhen_li@brown.edu
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <ctime>
 #include "pair_mdpd.h"
+#include <mpi.h>
+#include <cmath>
+#include <ctime>
 #include "atom.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp
index 2fd238088c..05cb123f61 100644
--- a/src/USER-MESO/pair_mdpd_rhosum.cpp
+++ b/src/USER-MESO/pair_mdpd_rhosum.cpp
@@ -19,9 +19,8 @@
    Contributing author: Zhen Li (Brown University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_mdpd_rhosum.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
@@ -30,8 +29,6 @@
 #include "memory.h"
 #include "error.h"
 #include "neighbor.h"
-#include "update.h"
-#include "domain.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp
index 7df9d6d163..346401b1ba 100644
--- a/src/USER-MESO/pair_tdpd.cpp
+++ b/src/USER-MESO/pair_tdpd.cpp
@@ -16,13 +16,10 @@
    Email: zhen_li@brown.edu
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <ctime>
 #include "pair_tdpd.h"
+#include <cmath>
+#include <ctime>
 #include "atom.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/USER-MGPT/mgpt_linalg.cpp b/src/USER-MGPT/mgpt_linalg.cpp
index 68701037f4..bc15873739 100644
--- a/src/USER-MGPT/mgpt_linalg.cpp
+++ b/src/USER-MGPT/mgpt_linalg.cpp
@@ -20,8 +20,6 @@
 
 #include <cstdio>
 #include <cstdlib>
-#include <cmath>
-#include <cassert>
 
 #define restrict __restrict__
 
diff --git a/src/USER-MGPT/mgpt_readpot.h b/src/USER-MGPT/mgpt_readpot.h
index c19ea40774..8f46592e8a 100644
--- a/src/USER-MGPT/mgpt_readpot.h
+++ b/src/USER-MGPT/mgpt_readpot.h
@@ -20,7 +20,8 @@
 #define READPOT__
 
 #include <cstdio>
-
+#include <cstdlib>
+#include <cstring>
 #include "mgpt_splinetab.h"
 
 struct potdata {
diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp
index 91c624eec5..0634872c70 100644
--- a/src/USER-MGPT/pair_mgpt.cpp
+++ b/src/USER-MGPT/pair_mgpt.cpp
@@ -21,17 +21,16 @@
    (2011).  See LLNL copyright notice at bottom of this file.
 ------------------------------------------------------------------------- */
 
+#include "pair_mgpt.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 #include <cassert>
 
-#include "pair_mgpt.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
-#include "memory.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
diff --git a/src/USER-MGPT/pair_mgpt.h b/src/USER-MGPT/pair_mgpt.h
index 94c66fb603..ff71edc9f3 100644
--- a/src/USER-MGPT/pair_mgpt.h
+++ b/src/USER-MGPT/pair_mgpt.h
@@ -30,9 +30,7 @@ PairStyle(mgpt,PairMGPT)
 #ifndef LMP_PAIR_MGPT_H
 #define LMP_PAIR_MGPT_H
 
-#include <new>
-#include <cmath>
-#include <cstdio>
+#include <cstdlib>
 #include <cassert>
 
 #include "pair.h"
@@ -78,29 +76,29 @@ public:
       Link(const K &k,Link *n) : next(n),key(k),hits(1) {}
 
       static void *operator new(std::size_t sz) {
-	const size_t align = 32;
-	size_t x = (size_t) (void *) ::operator new(sz+align);
-	size_t y = (x + align) - ((x+align)&(align-1));
-	assert(sizeof(void *) <= align);
-	assert((x & (sizeof(void *)-1)) == 0);
-	((void **) y)[-1] = (void *) x;
-	return (void *) y;
+        const size_t align = 32;
+        size_t x = (size_t) (void *) ::operator new(sz+align);
+        size_t y = (x + align) - ((x+align)&(align-1));
+        assert(sizeof(void *) <= align);
+        assert((x & (sizeof(void *)-1)) == 0);
+        ((void **) y)[-1] = (void *) x;
+        return (void *) y;
       }
       static void operator delete(void *ptr) {
-	::operator delete(((void **) ptr)[-1]);
+        ::operator delete(((void **) ptr)[-1]);
       }
     };
 
     int isprime(int x) {
       if(x%2 == 0)
-	return 0;
+        return 0;
       else {
-	int k = 3;
-	while(k*k <= x) {
-	  if(x%k == 0) return 0;
-	  k = k+2;
-	}
-	return 1;
+        int k = 3;
+        while(k*k <= x) {
+          if(x%k == 0) return 0;
+          k = k+2;
+        }
+        return 1;
     }
   }
 
@@ -118,25 +116,25 @@ public:
       Iterator(Hash &HH) : H(HH),idx(-1),p(0) { next(); }
       Iterator(Hash &HH,int iidx,Link *pp) : H(HH),idx(iidx),p(pp) {}
       void next() {
-	if(idx >= H.Size()) return;
-	if(p != 0) p = p->next;
-	if(p == 0) {
-	  do {
-	    idx = idx+1;
-	    if(idx >= H.Size()) return;
-	    p = H.table[idx];
-	  } while(p == 0);
-	}
+        if(idx >= H.Size()) return;
+        if(p != 0) p = p->next;
+        if(p == 0) {
+          do {
+            idx = idx+1;
+            if(idx >= H.Size()) return;
+            p = H.table[idx];
+          } while(p == 0);
+        }
       }
       K *key() { return &p->key; }
       T *data() { return &p->data; }
       Link *link() { return p; }
 
       int operator==(const Iterator &a) {
-	return idx==a.idx && p==a.p;
+        return idx==a.idx && p==a.p;
       }
       int operator!=(const Iterator &a) {
-	return !(*this == a);
+        return !(*this == a);
       }
     };
 
@@ -148,7 +146,7 @@ public:
 
       table = new Link *[size];
       for(int i = 0; i<size; i++)
-	table[i] = 0;
+        table[i] = 0;
 
       /* Counters for statistics */
       maxlength = 0;
@@ -158,12 +156,12 @@ public:
 
     ~Hash() {
       for(int i = 0; i<size; i++) {
-	Link *p = table[i];
-	while(p != 0) {
-	  Link *q = p->next;
-	delete p;
-	p = q;
-	}
+        Link *p = table[i];
+        while(p != 0) {
+          Link *q = p->next;
+        delete p;
+        p = q;
+        }
       }
       delete[] table;
     }
@@ -180,24 +178,24 @@ public:
       int idx = key.hash() % size;
       if(idx < 0) idx = idx + size;
       if(idx >= size || idx < 0) {
-	printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
-	exit(1);
+        printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
+        exit(1);
       }
 
       used = used + 1;
       if(1) {
-	table[idx] = new Link(key,table[idx]);
-	return &table[idx]->data;
+        table[idx] = new Link(key,table[idx]);
+        return &table[idx]->data;
       } else { /* This is for threading... and incomplete */
-	typedef Link *LinkPtr;
-	LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0);
+        typedef Link *LinkPtr;
+        LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0);
 
-	while(ptr != 0) {
-	  last = ptr;
-	  ptr = ptr->next;
-	}
-	*((volatile LinkPtr *) &(last->next)) = dataptr;
-	return &(dataptr->data);
+        while(ptr != 0) {
+          last = ptr;
+          ptr = ptr->next;
+        }
+        *((volatile LinkPtr *) &(last->next)) = dataptr;
+        return &(dataptr->data);
       }
     }
     void Remove(const K &key) {
@@ -206,28 +204,28 @@ public:
       int count = 1;
       if(idx < 0) idx = idx + size;
       if(idx >= size || idx < 0) {
-	printf("(2) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
-	exit(1);
+        printf("(2) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
+        exit(1);
       }
 
       p = table[idx];
       while(p != 0 && !(p->key == key)) {
-	last = p;
-	p = p->next;
-	count = count + 1;
+        last = p;
+        p = p->next;
+        count = count + 1;
       }
 
       if(p != 0) {
-	used = used - 1;
-	if(last == 0)
-	  table[idx] = p->next;
-	else
-	  last->next = p->next;
-	delete p;
+        used = used - 1;
+        if(last == 0)
+          table[idx] = p->next;
+        else
+          last->next = p->next;
+        delete p;
       }
 
       if(count > maxlength)
-	maxlength = count;
+        maxlength = count;
       nsearch = nsearch + 1;
       nstep = nstep + count;
     }
@@ -237,19 +235,19 @@ public:
       int count = 1;
       if(idx < 0) idx = idx + size;
       if(idx >= size || idx < 0) {
-	printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
-	exit(1);
+        printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
+        exit(1);
       }
 
 
       p = table[idx];
       while(p != 0 && !(p->key == key)) {
-	p = p->next;
-	count = count + 1;
+        p = p->next;
+        count = count + 1;
       }
 
       if(count > maxlength)
-	maxlength = count;
+        maxlength = count;
       nsearch = nsearch + 1;
       nstep = nstep + count;
 
@@ -284,46 +282,46 @@ public:
     }
     void zero() {
       for(int i = 0; i<8; i++)
-	for(int j = 0; j<8; j++)
-	  m[i][j] = 0.0;
+        for(int j = 0; j<8; j++)
+          m[i][j] = 0.0;
     }
 
     void operator=(const Matrix &A) {
       for(int i = 1; i<=sz; i++)
-	for(int j = 1; j<=sz; j++)
-	  m[i][j] = A.m[i][j];
+        for(int j = 1; j<=sz; j++)
+          m[i][j] = A.m[i][j];
     }
     void operator=(double x) {
       for(int i = 1; i<=sz; i++)
-	for(int j = 1; j<=sz; j++)
-	  m[i][j] = x;
+        for(int j = 1; j<=sz; j++)
+          m[i][j] = x;
     }
     Matrix operator+(const Matrix &B) const {
       Matrix s;
       for(int i = 1; i<=sz; i++)
-	for(int j = 1; j<=sz; j++)
-	  s.m[i][j] = m[i][j] + B.m[i][j];
+        for(int j = 1; j<=sz; j++)
+          s.m[i][j] = m[i][j] + B.m[i][j];
       return s;
     }
     Matrix operator-(const Matrix &B) const {
       Matrix s;
       for(int i = 1; i<=sz; i++)
-	for(int j = 1; j<=sz; j++)
-	  s.m[i][j] = m[i][j] - B.m[i][j];
+        for(int j = 1; j<=sz; j++)
+          s.m[i][j] = m[i][j] - B.m[i][j];
       return s;
     }
     Matrix operator-() const {
       Matrix s;
       for(int i = 1; i<=sz; i++)
-	for(int j = 1; j<=sz; j++)
-	  s.m[i][j] =  -m[i][j];
+        for(int j = 1; j<=sz; j++)
+          s.m[i][j] =  -m[i][j];
       return s;
     }
     Matrix operator*(double x) const {
       Matrix P;
       for(int i = 1; i<=sz; i++)
-	for(int j = 0; j<=sz; j++)
-	  P.m[i][j] = m[i][j] * x;
+        for(int j = 0; j<=sz; j++)
+          P.m[i][j] = m[i][j] * x;
       return P;
     }
     Matrix operator/(double x) const {
@@ -332,8 +330,8 @@ public:
     Matrix transpose() const {
       Matrix T;
       for(int i = 1; i<=sz; i++)
-	for(int j = 1; j<=sz; j++)
-	  T.m[j][i] = m[i][j];
+        for(int j = 1; j<=sz; j++)
+          T.m[j][i] = m[i][j];
       return T;
     }
   };
@@ -375,13 +373,13 @@ public:
 
     int align_check() {
       return
-	(H1H2.align_check()  << 0) |
-	(H1xH2.align_check() << 1) |
-	(H1yH2.align_check() << 2) |
-	(H1zH2.align_check() << 3) |
-	(H1H2x.align_check() << 4) |
-	(H1H2y.align_check() << 5) |
-	(H1H2z.align_check() << 6) ;
+        (H1H2.align_check()  << 0) |
+        (H1xH2.align_check() << 1) |
+        (H1yH2.align_check() << 2) |
+        (H1zH2.align_check() << 3) |
+        (H1H2x.align_check() << 4) |
+        (H1H2y.align_check() << 5) |
+        (H1H2z.align_check() << 6) ;
     }
 
     void zero() {
@@ -397,18 +395,18 @@ public:
   void make_bond(const double xx[][3],int i,int j,bond_data *bptr);
   void make_triplet(bond_data *ij_bond,bond_data *ik_bond,triplet_data *triptr);
   triplet_data *get_triplet(const double xx[][3],int i,int j,int k,
-			    Hash<bond_data,Doublet> *bhash,triplet_data *twork,
-			    double *dvir_ij_p,double *dvir_ik_p);
+                            Hash<bond_data,Doublet> *bhash,triplet_data *twork,
+                            double *dvir_ij_p,double *dvir_ik_p);
 
   int c1_outside(const double a[3],
-		 int triclinic,const double alpha[3]) {
+                 int triclinic,const double alpha[3]) {
     const double stol = 1e-5;
 
     if(triclinic) {
       for(int p = 0; p<3; p++) {
-	double cog = a[p];
-	if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1;
-	if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1;
+        double cog = a[p];
+        if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1;
+        if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1;
       }
 
     } else {
@@ -416,63 +414,63 @@ public:
 
 
       for(int p = 0; p<3; p++) {
-	double cog = a[p];
-	if(cog < domain->sublo[p]-0.5*rmax-stol) return 1;
-	if(cog > domain->subhi[p]+0.5*rmax+stol) return 1;
+        double cog = a[p];
+        if(cog < domain->sublo[p]-0.5*rmax-stol) return 1;
+        if(cog > domain->subhi[p]+0.5*rmax+stol) return 1;
 
-	if(cog < domain->sublo[p]-stol) {
-	  double t = cog - (domain->sublo[p]-stol);
-	  rout = rout + t*t;
-	} else if(cog > domain->subhi[p]+stol) {
-	  double t = cog - (domain->subhi[p]+stol);
-	  rout = rout + t*t;
-	}
+        if(cog < domain->sublo[p]-stol) {
+          double t = cog - (domain->sublo[p]-stol);
+          rout = rout + t*t;
+        } else if(cog > domain->subhi[p]+stol) {
+          double t = cog - (domain->subhi[p]+stol);
+          rout = rout + t*t;
+        }
 
       }
 
       if(rout > 0.25*rmax*rmax)
-	return 1;
+        return 1;
     }
 
     return 0;
   }
   int c2_outside(const double a[3],const double b[3],
-		 int triclinic,const double alpha[3]) {
+                 int triclinic,const double alpha[3]) {
     const double stol = 1e-5;
 
     if(triclinic) {
       for(int p = 0; p<3; p++) {
-	double cog = 0.5*(a[p] + b[p]);
-	if(cog < domain->sublo_lamda[p]-0.5*rcrit*alpha[p]-stol) return 1;
-	if(cog > domain->subhi_lamda[p]+0.5*rcrit*alpha[p]+stol) return 1;
+        double cog = 0.5*(a[p] + b[p]);
+        if(cog < domain->sublo_lamda[p]-0.5*rcrit*alpha[p]-stol) return 1;
+        if(cog > domain->subhi_lamda[p]+0.5*rcrit*alpha[p]+stol) return 1;
       }
     } else {
       double rout = 0.0;
 
       for(int p = 0; p<3; p++) {
-	double cog = 0.5*(a[p] + b[p]);
-	if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1;
-	if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1;
+        double cog = 0.5*(a[p] + b[p]);
+        if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1;
+        if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1;
 
-	if(cog < domain->sublo[p]-stol) {
-	  double t = cog - (domain->sublo[p]-stol);
-	  rout = rout + t*t;
-	} else if(cog > domain->subhi[p]+stol) {
-	  double t = cog - (domain->subhi[p]+stol);
-	  rout = rout + t*t;
-	}
+        if(cog < domain->sublo[p]-stol) {
+          double t = cog - (domain->sublo[p]-stol);
+          rout = rout + t*t;
+        } else if(cog > domain->subhi[p]+stol) {
+          double t = cog - (domain->subhi[p]+stol);
+          rout = rout + t*t;
+        }
 
       }
 
       if(rout > 0.25*rcrit*rcrit)
-	return 1;
+        return 1;
     }
 
     return 0;
   }
   double get_weight(const int triclinic,
-		    const double a[3] = 0,const double b[3] = 0,
-		    const double c[3] = 0,const double d[3] = 0) {
+                    const double a[3] = 0,const double b[3] = 0,
+                    const double c[3] = 0,const double d[3] = 0) {
     const double
       *s0 = triclinic ? domain->sublo_lamda : domain->sublo,
       *s1 = triclinic ? domain->subhi_lamda : domain->subhi;
@@ -499,46 +497,46 @@ public:
   }
 
   void force_debug_3t(double xx[][3],
-		      int i0,int j0,int k0,
-		      int i ,int j ,int k ,
-		      double dfix,double dfiy,double dfiz,
-		      double dfjx,double dfjy,double dfjz,
-		      double dfkx,double dfky,double dfkz);
+                      int i0,int j0,int k0,
+                      int i ,int j ,int k ,
+                      double dfix,double dfiy,double dfiz,
+                      double dfjx,double dfjy,double dfjz,
+                      double dfkx,double dfky,double dfkz);
 
   void force_debug_3v(double xx[][3],
-		      int i0,int j0,int k0,
-		      int i ,int j ,int k ,
-		      double dfix,double dfiy,double dfiz,
-		      double dfjx,double dfjy,double dfjz,
-		      double dfkx,double dfky,double dfkz);
+                      int i0,int j0,int k0,
+                      int i ,int j ,int k ,
+                      double dfix,double dfiy,double dfiz,
+                      double dfjx,double dfjy,double dfjz,
+                      double dfkx,double dfky,double dfkz);
 
   void force_debug_4(double xx[][3],
-		     int i0,int j0,int k0,int m0,
-		     int i ,int j ,int k ,int m ,
-		     double dfix,double dfiy,double dfiz,
-		     double dfjx,double dfjy,double dfjz,
-		     double dfkx,double dfky,double dfkz,
-		     double dfmx,double dfmy,double dfmz);
+                     int i0,int j0,int k0,int m0,
+                     int i ,int j ,int k ,int m ,
+                     double dfix,double dfiy,double dfiz,
+                     double dfjx,double dfjy,double dfjz,
+                     double dfkx,double dfky,double dfkz,
+                     double dfmx,double dfmy,double dfmz);
 
   double numderiv3t(double xx[][3],int i,int j,int k,int p);
   double numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert);
   double numderiv4(double xx[][3],int i,int j,int k,int m,int p);
   void compute_x(const int *nnei,const int * const *nlist,
-		 double *e_s,double *e_p,double *e_t,double *e_q,
-		 int evflag,int newton_pair);
+                 double *e_s,double *e_p,double *e_t,double *e_q,
+                 int evflag,int newton_pair);
 
   /* Reimplementation of bond matrix computation */
   void fl_deriv_new(double r,double ri,double xhat,double yhat,double zhat,
-		    double &fl_0,double &fl_x,double &fl_y,double &fl_z,
-		    double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al);
+                    double &fl_0,double &fl_x,double &fl_y,double &fl_z,
+                    double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al);
   void hamltn_5_raw(const double xin,const double yin,const double zin,
-		    double M [8][8],double Mx[8][8],
-		    double My[8][8],double Mz[8][8],
-		    double *fl_deriv_sum_p);
+                    double M [8][8],double Mx[8][8],
+                    double My[8][8],double Mz[8][8],
+                    double *fl_deriv_sum_p);
   void hamltn_7_raw(const double xin,const double yin,const double zin,
-		    double M [8][8],double Mx[8][8],
-		    double My[8][8],double Mz[8][8],
-		    double *fl_deriv_sum_p);
+                    double M [8][8],double Mx[8][8],
+                    double My[8][8],double Mz[8][8],
+                    double *fl_deriv_sum_p);
   /* * */
   // Old matrix routines, only used in force debug routines.
 
@@ -547,9 +545,9 @@ public:
     Matrix h;
     for(int l = 1; l <= lmax; l++) {
       for(int n = 1; n <= lmax; n++) {
-	h.m[l][n] = 0.0;
-	for(int m = 1; m <= lmax; m++)
-	  h.m[l][n] += ha.m[l][m] * hb.m[m][n];
+        h.m[l][n] = 0.0;
+        for(int m = 1; m <= lmax; m++)
+          h.m[l][n] += ha.m[l][m] * hb.m[m][n];
       }
     }
     return h;
@@ -561,7 +559,7 @@ public:
     for(int n = 1; n <= lmax; n++) {
       double cquan = 0.0;
       for(int m = 1; m <= lmax; m++)
-	cquan += ha.m[n][m] * hb.m[m][n];
+        cquan += ha.m[n][m] * hb.m[m][n];
       zquan += cquan;
     }
     return zquan;
@@ -573,32 +571,32 @@ public:
       int i,j,k;
 
       if(lmax == 5) {
-	const int n = 5;
-	for(i = 1; i<=n; i++)
-	  for(j = 1; j<=n; j++) {
-	    double s = 0.0;
-	    for(k = 1; k<=n; k++)
-	      s = s + a.m[i][k]*b.m[j][k];
-	    c.m[i][j] = s;
-	      }
+        const int n = 5;
+        for(i = 1; i<=n; i++)
+          for(j = 1; j<=n; j++) {
+            double s = 0.0;
+            for(k = 1; k<=n; k++)
+              s = s + a.m[i][k]*b.m[j][k];
+            c.m[i][j] = s;
+              }
       } else if(lmax == 7) {
-	const int n = 7;
-	for(i = 1; i<=n; i++)
-	  for(j = 1; j<=n; j++) {
-	    double s = 0.0;
-	    for(k = 1; k<=n; k++)
-	      s = s + a.m[i][k]*b.m[j][k];
-	    c.m[i][j] = s;
-	  }
+        const int n = 7;
+        for(i = 1; i<=n; i++)
+          for(j = 1; j<=n; j++) {
+            double s = 0.0;
+            for(k = 1; k<=n; k++)
+              s = s + a.m[i][k]*b.m[j][k];
+            c.m[i][j] = s;
+          }
       } else {
-	const int n = lmax;
-	for(i = 1; i<=n; i++)
-	  for(j = 1; j<=n; j++) {
-	    double s = 0.0;
-	    for(k = 1; k<=n; k++)
-	      s = s + a.m[i][k]*b.m[j][k];
-	    c.m[i][j] = s;
-	  }
+        const int n = lmax;
+        for(i = 1; i<=n; i++)
+          for(j = 1; j<=n; j++) {
+            double s = 0.0;
+            for(k = 1; k<=n; k++)
+              s = s + a.m[i][k]*b.m[j][k];
+            c.m[i][j] = s;
+          }
       }
     }
 
@@ -609,7 +607,7 @@ public:
 
     for(i = 0; i<n; i++)
       for(j = 1; j<=n; j++)
-	s = s + A[i][j]*B[i][j];
+        s = s + A[i][j]*B[i][j];
     return s;
   }
   inline double transtrace(const Matrix& a,const Matrix& b) const
@@ -618,25 +616,25 @@ public:
       double s = 0.0;
 
       if(linalg.single)
-	return transtrace_s((const float (*)[8]) &a.m[1][0],(const float (*)[8]) &b.m[1][0]);
+        return transtrace_s((const float (*)[8]) &a.m[1][0],(const float (*)[8]) &b.m[1][0]);
 
       //printf("Calling transtrace... That is shit\n");
 
       if(lmax == 5) {
-	const int n = 5;
-	for(i = 1; i<=n; i++)
-	  for(k = 1; k<=n; k++)
-	    s = s + a.m[i][k]*b.m[i][k];
+        const int n = 5;
+        for(i = 1; i<=n; i++)
+          for(k = 1; k<=n; k++)
+            s = s + a.m[i][k]*b.m[i][k];
       } else if(lmax == 7) {
-	const int n = 7;
-	for(i = 1; i<=n; i++)
-	  for(k = 1; k<=n; k++)
-	    s = s + a.m[i][k]*b.m[i][k];
+        const int n = 7;
+        for(i = 1; i<=n; i++)
+          for(k = 1; k<=n; k++)
+            s = s + a.m[i][k]*b.m[i][k];
       } else {
-	const int n = lmax;
-	for(i = 1; i<=n; i++)
-	  for(k = 1; k<=n; k++)
-	    s = s + a.m[i][k]*b.m[i][k];
+        const int n = lmax;
+        for(i = 1; i<=n; i++)
+          for(k = 1; k<=n; k++)
+            s = s + a.m[i][k]*b.m[i][k];
       }
       return s;
     }
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index 219e19673d..442feedf87 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -30,7 +30,10 @@ compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007
 compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013
 compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017
 compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018
+compute gyration/shape, Evangelos Voyiatzis, evoyiatzis at gmail.com, 25 July 2019
+compute hma, Andrew Schultz & David Kofke (UB), ajs42 at buffalo.edu & kofke at buffalo.edu, 1 Jul 2019
 compute pressure/cylinder, Cody K. Addington (NCSU), , 2 Oct 2018
+compute momentum, Rupert Nash (University of Edinburgh), r.nash at epcc.ed.ac.uk, 28 June 2019
 compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18
 compute stress/mop/profile, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18
 compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
@@ -67,6 +70,7 @@ improper_style ring, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12
 improper_style distance, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
 pair_style agni, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 16
 pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
+pair_style cosine/squared, Eugen Rozic, eugen.rozic.17 at ucl.ac.uk, 9 Aug 19
 pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
 pair_style coul/shield, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18
 pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
diff --git a/src/USER-MISC/angle_cosine_shift.cpp b/src/USER-MISC/angle_cosine_shift.cpp
index 18c87c81e3..b18ddc79d3 100644
--- a/src/USER-MISC/angle_cosine_shift.cpp
+++ b/src/USER-MISC/angle_cosine_shift.cpp
@@ -15,9 +15,9 @@
    Contributing author: Carsten Svaneborg, science@zqex.dk
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_cosine_shift.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/USER-MISC/angle_cosine_shift.h b/src/USER-MISC/angle_cosine_shift.h
index 030709a0e2..febabcc090 100644
--- a/src/USER-MISC/angle_cosine_shift.h
+++ b/src/USER-MISC/angle_cosine_shift.h
@@ -20,7 +20,6 @@ AngleStyle(cosine/shift,AngleCosineShift)
 #ifndef LMP_ANGLE_COSINE_SHIFT_H
 #define LMP_ANGLE_COSINE_SHIFT_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp
index 8c6282de20..79cb0fea7c 100644
--- a/src/USER-MISC/angle_cosine_shift_exp.cpp
+++ b/src/USER-MISC/angle_cosine_shift_exp.cpp
@@ -15,9 +15,9 @@
    Contributing author: Carsten Svaneborg, science@zqex.dk
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_cosine_shift_exp.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/USER-MISC/angle_cosine_shift_exp.h b/src/USER-MISC/angle_cosine_shift_exp.h
index 8b8e389380..9614ddcc19 100644
--- a/src/USER-MISC/angle_cosine_shift_exp.h
+++ b/src/USER-MISC/angle_cosine_shift_exp.h
@@ -18,7 +18,6 @@ AngleStyle(cosine/shift/exp,AngleCosineShiftExp)
 #ifndef LMP_ANGLE_COSINE_SHIFT_EXP_H
 #define LMP_ANGLE_COSINE_SHIFT_EXP_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp
index 781da46869..0956ba3b8f 100644
--- a/src/USER-MISC/angle_dipole.cpp
+++ b/src/USER-MISC/angle_dipole.cpp
@@ -15,9 +15,9 @@
    Contributing authors: Mario Orsi & Wei Ding (QMUL), m.orsi@qmul.ac.uk
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_dipole.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/USER-MISC/angle_dipole.h b/src/USER-MISC/angle_dipole.h
index 6c5dccb803..187822d0d4 100644
--- a/src/USER-MISC/angle_dipole.h
+++ b/src/USER-MISC/angle_dipole.h
@@ -20,7 +20,6 @@ AngleStyle(dipole,AngleDipole)
 #ifndef LMP_ANGLE_DIPOLE_H
 #define LMP_ANGLE_DIPOLE_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp
index 8f5074ff5d..dcf5080431 100644
--- a/src/USER-MISC/angle_fourier.cpp
+++ b/src/USER-MISC/angle_fourier.cpp
@@ -16,9 +16,9 @@
    [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)]
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_fourier.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/USER-MISC/angle_fourier.h b/src/USER-MISC/angle_fourier.h
index 14b4eedf57..53eeea98da 100644
--- a/src/USER-MISC/angle_fourier.h
+++ b/src/USER-MISC/angle_fourier.h
@@ -20,7 +20,6 @@ AngleStyle(fourier,AngleFourier)
 #ifndef ANGLE_FOURIER_H
 #define ANGLE_FOURIER_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp
index 615556bbe7..bbe3f8520b 100644
--- a/src/USER-MISC/angle_fourier_simple.cpp
+++ b/src/USER-MISC/angle_fourier_simple.cpp
@@ -16,9 +16,9 @@
    [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)]
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_fourier_simple.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/USER-MISC/angle_fourier_simple.h b/src/USER-MISC/angle_fourier_simple.h
index 3a7bd37750..df2253317f 100644
--- a/src/USER-MISC/angle_fourier_simple.h
+++ b/src/USER-MISC/angle_fourier_simple.h
@@ -20,7 +20,6 @@ AngleStyle(fourier/simple,AngleFourierSimple)
 #ifndef ANGLE_FOURIER_SIMPLE_H
 #define ANGLE_FOURIER_SIMPLE_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp
index 21a96100aa..5c5f3411e4 100644
--- a/src/USER-MISC/angle_quartic.cpp
+++ b/src/USER-MISC/angle_quartic.cpp
@@ -16,9 +16,9 @@
    [ based on angle_harmonic.cpp]
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_quartic.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/USER-MISC/angle_quartic.h b/src/USER-MISC/angle_quartic.h
index 7043cab064..b916a5f89f 100644
--- a/src/USER-MISC/angle_quartic.h
+++ b/src/USER-MISC/angle_quartic.h
@@ -20,7 +20,6 @@ AngleStyle(quartic,AngleQuartic)
 #ifndef LMP_ANGLE_QUARTIC_H
 #define LMP_ANGLE_QUARTIC_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp
index c7e4444cce..fdd3111783 100644
--- a/src/USER-MISC/bond_harmonic_shift.cpp
+++ b/src/USER-MISC/bond_harmonic_shift.cpp
@@ -15,12 +15,11 @@
    Contributing author: Carsten Svaneborg, science@zqex.dk
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "bond_harmonic_shift.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/USER-MISC/bond_harmonic_shift.h b/src/USER-MISC/bond_harmonic_shift.h
index ff0d358243..b77cefb4af 100644
--- a/src/USER-MISC/bond_harmonic_shift.h
+++ b/src/USER-MISC/bond_harmonic_shift.h
@@ -20,7 +20,6 @@ BondStyle(harmonic/shift,BondHarmonicShift)
 #ifndef LMP_BOND_HARMONIC_SHIFT_H
 #define LMP_BOND_HARMONIC_SHIFT_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp
index 5b396f5d72..0688cb428a 100644
--- a/src/USER-MISC/bond_harmonic_shift_cut.cpp
+++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp
@@ -15,12 +15,11 @@
    Contributing author: Carsten Svaneborg, science@zqex.dk
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "bond_harmonic_shift_cut.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/USER-MISC/bond_harmonic_shift_cut.h b/src/USER-MISC/bond_harmonic_shift_cut.h
index 5db76d51aa..ad2bcd61ad 100644
--- a/src/USER-MISC/bond_harmonic_shift_cut.h
+++ b/src/USER-MISC/bond_harmonic_shift_cut.h
@@ -20,7 +20,6 @@ BondStyle(harmonic/shift/cut,BondHarmonicShiftCut)
 #ifndef LMP_BOND_HARMONIC_SHIFT_CUT_H
 #define LMP_BOND_HARMONIC_SHIFT_CUT_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp
index 6fa16f1a9a..ba97be25d4 100644
--- a/src/USER-MISC/compute_cnp_atom.cpp
+++ b/src/USER-MISC/compute_cnp_atom.cpp
@@ -21,11 +21,10 @@
    branicio@usc.edu
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
-
 #include "compute_cnp_atom.h"
+#include <mpi.h>
+#include <cstring>
+#include <cmath>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/USER-MISC/compute_entropy_atom.cpp b/src/USER-MISC/compute_entropy_atom.cpp
index 0367d7fe6d..00f7e6dc8b 100644
--- a/src/USER-MISC/compute_entropy_atom.cpp
+++ b/src/USER-MISC/compute_entropy_atom.cpp
@@ -15,10 +15,9 @@
    Contributing author: Pablo Piaggi (EPFL Lausanne)
 ------------------------------------------------------------------------- */
 
+#include "compute_entropy_atom.h"
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "compute_entropy_atom.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
@@ -28,13 +27,11 @@
 #include "force.h"
 #include "pair.h"
 #include "comm.h"
-#include "math_extra.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "domain.h"
 
-
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
diff --git a/src/USER-MISC/compute_gyration_shape.cpp b/src/USER-MISC/compute_gyration_shape.cpp
new file mode 100644
index 0000000000..a0ee6089b7
--- /dev/null
+++ b/src/USER-MISC/compute_gyration_shape.cpp
@@ -0,0 +1,130 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ *    Contributing author:  Evangelos Voyiatzis (Royal DSM)
+ * ------------------------------------------------------------------------- */
+
+
+#include "compute_gyration_shape.h"
+#include <cmath>
+#include <cstring>
+#include "error.h"
+#include "math_extra.h"
+#include "math_special.h"
+#include "modify.h"
+#include "update.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeGyrationShape::ComputeGyrationShape(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg), id_gyration(NULL)
+{
+  if (narg != 4) error->all(FLERR,"Illegal compute gyration/shape command");
+
+  vector_flag = 1;
+  size_vector = 6;
+  extscalar = 0;
+  extvector = 0;
+
+  // ID of compute gyration 
+  int n = strlen(arg[3]) + 1;
+  id_gyration = new char[n];
+  strcpy(id_gyration,arg[3]);
+
+  init();
+
+  vector = new double[6];
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeGyrationShape::~ComputeGyrationShape()
+{
+  delete [] id_gyration;
+  delete [] vector;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeGyrationShape::init()
+{
+  // check that the compute gyration command exist
+  int icompute = modify->find_compute(id_gyration);
+  if (icompute < 0)
+    error->all(FLERR,"Compute gyration ID does not exist for "
+               "compute gyration/shape");
+
+  // check the id_gyration corresponds really to a compute gyration command
+  c_gyration = (Compute *) modify->compute[icompute];
+  if (strcmp(c_gyration->style,"gyration") != 0)
+    error->all(FLERR,"Compute gyration compute ID does not point to "
+               "gyration compute for compute gyration/shape");
+}
+
+/* ----------------------------------------------------------------------
+   compute shape parameters based on the eigenvalues of the
+   gyration tensor of group of atoms
+------------------------------------------------------------------------- */
+
+void ComputeGyrationShape::compute_vector()
+{
+  invoked_vector = update->ntimestep;
+  c_gyration->compute_vector();
+  double *gyration_tensor = c_gyration->vector;
+
+  // call the function for the calculation of the eigenvalues
+  double ione[3][3], evalues[3], evectors[3][3];
+
+  ione[0][0] = gyration_tensor[0];
+  ione[1][1] = gyration_tensor[1];
+  ione[2][2] = gyration_tensor[2];
+  ione[0][1] = ione[1][0] = gyration_tensor[3];
+  ione[1][2] = ione[2][1] = gyration_tensor[4];
+  ione[0][2] = ione[2][0] = gyration_tensor[5];
+
+  int ierror = MathExtra::jacobi(ione,evalues,evectors);
+  if (ierror) error->all(FLERR, "Insufficient Jacobi rotations "
+                         "for gyration/shape");
+
+  // sort the eigenvalues according to their size with bubble sort
+  double t;
+  for (int i = 0; i < 3; i++) {
+    for (int j = 0; j < 2-i; j++) {
+      if (fabs(evalues[j]) < fabs(evalues[j+1])) {
+        t = evalues[j];
+        evalues[j] = evalues[j+1];
+        evalues[j+1] = t;
+      }
+    }
+  }
+
+  // compute the shape parameters of the gyration tensor
+  double sq_eigen_x = MathSpecial::square(evalues[0]);
+  double sq_eigen_y = MathSpecial::square(evalues[1]);
+  double sq_eigen_z = MathSpecial::square(evalues[2]);
+
+  double nominator = MathSpecial::square(sq_eigen_x)
+    + MathSpecial::square(sq_eigen_y)
+    + MathSpecial::square(sq_eigen_z);
+  double denominator = MathSpecial::square(sq_eigen_x+sq_eigen_y+sq_eigen_z);
+
+  vector[0] = evalues[0];
+  vector[1] = evalues[1];
+  vector[2] = evalues[2];
+  vector[3] = sq_eigen_z - 0.5*(sq_eigen_x + sq_eigen_y);
+  vector[4] = sq_eigen_y - sq_eigen_x;
+  vector[5] = 0.5*(3*nominator/denominator - 1.0);
+}
diff --git a/src/USER-MISC/compute_gyration_shape.h b/src/USER-MISC/compute_gyration_shape.h
new file mode 100644
index 0000000000..1d58f000dd
--- /dev/null
+++ b/src/USER-MISC/compute_gyration_shape.h
@@ -0,0 +1,60 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(gyration/shape,ComputeGyrationShape)
+
+#else
+
+#ifndef LMP_COMPUTE_GYRATION_SHAPE_H
+#define LMP_COMPUTE_GYRATION_SHAPE_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeGyrationShape : public Compute {
+ public:
+  char *id_gyration;              // fields accessed by other classes
+
+  ComputeGyrationShape(class LAMMPS *, int, char **);
+  ~ComputeGyrationShape();
+  void init();
+  void compute_vector();
+
+ private:
+  class Compute *c_gyration;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Compute gyration ID does not exist for compute gyration/shape
+
+Self-explanatory.  Provide a valid compute ID
+
+E: Compute gyration/shape compute ID does not point to a gyration compute
+
+Self-explanatory.  Provide an ID of a compute gyration command.
+*/
diff --git a/src/USER-MISC/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp
new file mode 100644
index 0000000000..a14084b9ca
--- /dev/null
+++ b/src/USER-MISC/compute_hma.cpp
@@ -0,0 +1,516 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+This compute implements harmonically-mapped averaging for crystalline solids.
+The current implementation handles atomic crystals.
+
+Computing the heat capacity relies on being able to compute the second
+derivative of the energy with respect to atom positions.  This capability is
+provided by the single2 method in Pair, but is currently only implemented for
+the shifted-force LJ potential (lj/smooth/linear).  Pair::single2 takes a single
+pair and (like Pair::single) returns the energy and sets the force as an out
+parameter, but also sets the elements of 6-element double array out parameter,
+which are the unique components of the atomic Hessian tensor for the pair.  A
+helper method exists (Pair::pairTensor), which will compute the tensor from
+linear derivatives and the vector between the positions.  HMA Heat capacity can
+be computed for other models by implementing single2 in those Pair classes.
+
+More information about HMA is available in these publications:
+
+A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy
+equation of state and coexistence properties for classical Lennard-Jones
+crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018)
+https://dx.doi.org/10.1063/1.5053714
+
+S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for
+Computing the Free Energy of Classical Crystals by Molecular Simulation: A
+Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017)
+https://dx.doi.org/10.1021/acs.jctc.6b01082
+
+S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal
+properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015)
+https://dx.doi.org/10.1103/PhysRevE.92.043303
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstring>
+#include <mpi.h>
+#include "compute_hma.h"
+#include "atom.h"
+#include "update.h"
+#include "force.h"
+#include "pair.h"
+#include "bond.h"
+#include "angle.h"
+#include "dihedral.h"
+#include "improper.h"
+#include "kspace.h"
+#include "group.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "fix_store.h"
+#include "memory.h"
+#include "error.h"
+#include "comm.h"
+#include "neighbor.h"
+#include "neigh_request.h"
+#include "neigh_list.h"
+
+#include <vector>
+
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg), id_temp(NULL), deltaR(NULL)
+{
+  if (narg < 4) error->all(FLERR,"Illegal compute hma command");                    
+  if (igroup) error->all(FLERR,"Compute hma must use group all");
+  if (strcmp(arg[3],"NULL") == 0) {error->all(FLERR,"fix ID specifying the set temperature of canonical simulation is required");}       
+  else {
+    int n = strlen(arg[3]) + 1;                  
+    id_temp = new char[n];   
+    strcpy(id_temp,arg[3]);                         
+  }
+ 
+  create_attribute = 1;                  
+  extscalar = 1;                         
+  timeflag = 1;                         
+
+  // (from compute displace/atom) create a new fix STORE style  
+  // our new fix's id (id_fix)= compute-ID + COMPUTE_STORE 
+  // our new fix's group = same as compute group
+
+  int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
+  id_fix = new char[n];
+  strcpy(id_fix,id);
+  strcat(id_fix,"_COMPUTE_STORE");
+
+  char **newarg = new char*[6];     
+  newarg[0] = id_fix;
+  newarg[1] = group->names[igroup];
+  newarg[2] = (char *) "STORE";              
+  newarg[3] = (char *) "peratom";
+  newarg[4] = (char *) "1";
+  newarg[5] = (char *) "3";
+  modify->add_fix(6,newarg);        
+  fix = (FixStore *) modify->fix[modify->nfix-1];    
+ 
+  delete [] newarg;                               
+
+  // calculate xu,yu,zu for fix store array
+  // skip if reset from restart file
+
+  if (fix->restart_reset) fix->restart_reset = 0;   
+  else {
+    double **xoriginal = fix->astore;            
+    double **x = atom->x;
+    imageint *image = atom->image;
+    int nlocal = atom->nlocal;
+
+    for (int i = 0; i < nlocal; i++)
+      domain->unmap(x[i],image[i],xoriginal[i]);          
+  }
+
+  vector_flag = 1;
+  extvector = -1;
+  comm_forward = 0; // 3 if 2nd derivative needed
+
+  computeU = computeP = computeCv = -1;
+  returnAnharmonic = 0;
+  size_vector = 0;
+  memory->create(extlist, 3, "hma:extlist");
+  for (int iarg=4; iarg<narg; iarg++) {
+    if (!strcmp(arg[iarg], "u")) {
+      if (computeU>-1) continue;
+      computeU = size_vector;
+      extlist[size_vector] = 1;
+      size_vector++;
+    }
+    else if (!strcmp(arg[iarg], "p")) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal compute hma command");
+      if (computeP>-1) continue;
+      computeP = size_vector;
+      deltaPcap = force->numeric(FLERR, arg[iarg+1]);
+      extlist[size_vector] = 0;
+      size_vector++;
+      iarg++;
+    }
+    else if (!strcmp(arg[iarg], "cv")) {
+      if (computeCv>-1) continue;
+      computeCv = size_vector;
+      comm_forward = 3;
+      extlist[size_vector] = 1;
+      size_vector++;
+    }
+    else if (!strcmp(arg[iarg], "anharmonic")) {
+      // the first time we're called, we'll grab lattice pressure and energy
+      returnAnharmonic = -1;
+    }
+    else {
+      error->all(FLERR,"Illegal compute hma command");
+    }
+  }
+
+  if (size_vector == 0) {
+    error->all(FLERR,"Illegal compute hma command");
+  }
+  if (size_vector<3) {
+    memory->grow(extlist, size_vector, "hma:extlist");
+  }
+  memory->create(vector, size_vector, "hma:vector");
+
+  if (computeU>-1 || computeCv>-1) {
+    peflag = 1;                             
+  }
+  if (computeP>-1) {
+    pressflag = 1;
+  }
+
+  nmax = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeHMA::~ComputeHMA()
+{
+  // check nfix in case all fixes have already been deleted
+  if (modify->nfix) modify->delete_fix(id_fix);
+
+  delete [] id_fix;
+  delete [] id_temp;
+  memory->destroy(extlist);
+  memory->destroy(vector);
+  memory->destroy(deltaR);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeHMA::init() {
+  if (computeCv>-1) {
+    if (force->pair == NULL)
+      error->all(FLERR,"No pair style is defined for compute hma cv");
+    if (force->pair->single_enable == 0)
+      error->all(FLERR,"Pair style does not support compute hma cv");
+  }
+
+  int irequest = neighbor->request(this,instance_me);
+  neighbor->requests[irequest]->pair = 0; 
+  neighbor->requests[irequest]->compute = 1; 
+  neighbor->requests[irequest]->occasional = 1; 
+}
+
+void ComputeHMA::init_list(int id, NeighList *ptr)
+{
+  list = ptr;
+}
+
+void ComputeHMA::setup()
+{
+  int dummy=0;
+  int ifix = modify->find_fix(id_temp);
+  if (ifix < 0) error->all(FLERR,"Could not find compute hma temperature ID");
+  double * temperat = (double *) modify->fix[ifix]->extract("t_target",dummy);      
+  if (temperat==NULL) error->all(FLERR,"Could not find compute hma temperature ID");
+  finaltemp = * temperat;       
+
+  // set fix which stores original atom coords
+
+  int ifix2 = modify->find_fix(id_fix);
+  if (ifix2 < 0) error->all(FLERR,"Could not find hma store fix ID");
+  fix = (FixStore *) modify->fix[ifix2];             
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeHMA::compute_vector()
+{
+  invoked_vector = update->ntimestep;         
+
+  // grow deltaR array if necessary
+  if (comm_forward>0 && atom->nmax > nmax) {
+    memory->destroy(deltaR);
+    nmax = atom->nmax;
+    memory->create(deltaR,nmax,3,"hma:deltaR");
+  }
+
+  double **xoriginal = fix->astore;
+  double fdr = 0.0;
+  double **x = atom->x;
+  double **f = atom->f;
+
+  imageint *image = atom->image;
+  int nlocal = atom->nlocal;
+
+  double *h = domain->h;
+  double xprd = domain->xprd;   
+  double yprd = domain->yprd;
+  double zprd = domain->zprd;
+
+  double u = 0.0;
+  if (computeU>-1 || computeCv>-1) {
+    if (force->pair) u += force->pair->eng_vdwl + force->pair->eng_coul;
+    if (force->bond) u += force->bond->energy;
+    if (force->angle) u += force->angle->energy;
+    if (force->dihedral) u += force->dihedral->energy;
+    if (force->improper) u += force->improper->energy;
+  }
+
+  int dimension = domain->dimension;
+  double p = 0, vol = 0;
+  if (computeP>-1) {
+    p = virial_compute(dimension);
+    vol = xprd * yprd;
+    if (dimension == 3) vol *= zprd;
+    p *= force->nktv2p / (dimension*vol);
+    if (returnAnharmonic == -1) {
+      pLat = p;
+    }
+  }
+
+  if (domain->triclinic == 0) {
+    for (int i = 0; i < nlocal; i++) {
+      int xbox = (image[i] & IMGMASK) - IMGMAX;
+      int ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
+      int zbox = (image[i] >> IMG2BITS) - IMGMAX;
+      double dx = x[i][0] + xbox*xprd - xoriginal[i][0];
+      double dy = x[i][1] + ybox*yprd - xoriginal[i][1];
+      double dz = x[i][2] + zbox*zprd - xoriginal[i][2];
+      if (comm_forward>0) {
+        deltaR[i][0] = dx;
+        deltaR[i][1] = dy;
+        deltaR[i][2] = dz;
+      }
+      fdr += dx*f[i][0] + dy*f[i][1] + dz*f[i][2];
+    }
+  }
+  else {
+    for (int i = 0; i < nlocal; i++) {
+      int xbox = (image[i] & IMGMASK) - IMGMAX;
+      int ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
+      int zbox = (image[i] >> IMG2BITS) - IMGMAX;
+      double dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0];
+      double dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1];
+      double dz = x[i][2] + h[2]*zbox - xoriginal[i][2];
+      if (comm_forward>0) {
+        deltaR[i][0] = dx;
+        deltaR[i][1] = dy;
+        deltaR[i][2] = dz;
+      }
+      fdr += ((dx*f[i][0])+(dy*f[i][1])+(dz*f[i][2]));
+    }
+  }
+
+  double phiSum = 0.0;
+  if (computeCv>-1) {
+    comm->forward_comm_compute(this);
+    int *type = atom->type;
+    double** cutsq = force->pair->cutsq;
+    if (force->pair) {
+      double **x = atom->x;
+      double **f = atom->f;
+      int *type = atom->type;
+      int nlocal = atom->nlocal;
+      double *special_lj = force->special_lj;
+      double *special_coul = force->special_coul;
+      int newton_pair = force->newton_pair;
+
+      if (update->firststep == update->ntimestep) neighbor->build_one(list,1);
+      else neighbor->build_one(list);
+      int inum = list->inum;
+      int *ilist = list->ilist;
+      int *numneigh = list->numneigh;
+      int **firstneigh = list->firstneigh;
+
+      for (int ii = 0; ii < inum; ii++) {
+        int i = ilist[ii];
+        double fac = (newton_pair || i < nlocal) ? 1.0 : 0.5;
+        double* ix = x[i];
+        int itype = type[i];
+        int *jlist = firstneigh[i];
+        int jnum = numneigh[i];
+        double *idr = deltaR[i];
+        for (int jj = 0; jj < jnum; jj++) {
+          int j = jlist[jj];
+          if (!newton_pair && j>=nlocal) fac -= 0.5;
+          double factor_lj = special_lj[sbmask(j)];
+          double factor_coul = special_coul[sbmask(j)];
+          j &= NEIGHMASK;
+          double* jx = x[j];
+          double delr[3];
+          delr[0] = ix[0] - jx[0];
+          delr[1] = ix[1] - jx[1];
+          delr[2] = ix[2] - jx[2];
+          double rsq = delr[0]*delr[0] + delr[1]*delr[1] + delr[2]*delr[2];
+          int jtype = type[j];
+          if (rsq < cutsq[itype][jtype]) {
+            double* jdr = deltaR[j];
+            double fforce, d2u[6];
+            force->pair->single_hessian(i, j, itype, jtype, rsq, delr, factor_coul, factor_lj, fforce, d2u);
+            int m = 0;
+            for (int k=0; k<3; k++) {
+              double a = fac;
+              for (int l=k; l<3; l++) {
+                phiSum += a*(idr[k]*jdr[l]+jdr[k]*idr[l])*d2u[m];
+                phiSum -= a*(idr[k]*idr[l]*d2u[m] + jdr[k]*jdr[l]*d2u[m]);
+                m++;
+                if (k==l) a *= 2;
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+
+  // compute and sum up properties across processors
+
+  double fdrTotal;
+  MPI_Allreduce(&fdr,&fdrTotal,1,MPI_DOUBLE,MPI_SUM,world);
+  double uTotal;
+  if (computeU>-1 || computeCv>-1) {
+    MPI_Allreduce(&u,&uTotal,1,MPI_DOUBLE,MPI_SUM,world);
+    if (returnAnharmonic == -1) {
+      uLat = uTotal;
+    }
+    if (computeU>-1) {
+      if (returnAnharmonic) {
+        vector[computeU] = uTotal - uLat + 0.5*fdrTotal;
+      }
+      else {
+        vector[computeU] = uTotal + 0.5*fdrTotal + 0.5*dimension*(atom->natoms - 1)*force->boltz*finaltemp;
+      }
+    }
+  }
+
+  if (computeP>-1) {
+    double fv = ((deltaPcap)-(force->boltz*finaltemp*force->nktv2p*atom->natoms/vol))/(force->boltz*finaltemp*dimension*(atom->natoms - 1));
+    if (returnAnharmonic) {
+      vector[computeP] = p - pLat + (fv*fdrTotal);
+    }
+    else {
+      vector[computeP] = p + (fv*fdrTotal) + deltaPcap;
+    }
+  }
+
+  if (computeCv>-1) {
+    if (computeU==-1) MPI_Allreduce(&u,&uTotal,1,MPI_DOUBLE,MPI_SUM,world);
+    double buTot;
+    if (returnAnharmonic) {
+      buTot = (uTotal - uLat + 0.5*fdrTotal)/finaltemp;
+    }
+    else {
+      buTot = (uTotal + 0.5*fdrTotal)/finaltemp + 0.5*dimension*(atom->natoms - 1)*force->boltz;
+    }
+    double one = -0.25*(fdr + phiSum)/finaltemp;
+    double Cv;
+    MPI_Allreduce(&one,&Cv,1,MPI_DOUBLE,MPI_SUM,world);
+    vector[computeCv] = Cv + buTot*buTot;
+    if (!returnAnharmonic) {
+      vector[computeCv] += 0.5*dimension*(atom->natoms-1);
+    }
+  }
+  if (returnAnharmonic == -1) {
+    // we have our lattice properties
+    returnAnharmonic = 1;
+  }
+}
+
+double ComputeHMA::virial_compute(int n)
+{
+  double v = 0;
+
+  // sum contributions to virial from forces and fixes
+
+  if (force->pair) v += sumVirial(n, force->pair->virial);
+  if (force->bond) v += sumVirial(n, force->bond->virial);
+  if (force->angle) v += sumVirial(n, force->angle->virial);
+  if (force->dihedral) v += sumVirial(n, force->dihedral->virial);
+  if (force->improper) v += sumVirial(n, force->improper->virial);
+  for (int i = 0; i < modify->nfix; i++)
+    if (modify->fix[i]->thermo_virial) v += sumVirial(n, modify->fix[i]->virial);
+
+  // sum virial across procs
+
+  double virial;
+  MPI_Allreduce(&v,&virial,1,MPI_DOUBLE,MPI_SUM,world);
+
+  // KSpace virial contribution is already summed across procs
+
+  if (force->kspace)
+    for (int i = 0; i < n; i++) virial += force->kspace->virial[i];
+  return virial;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int ComputeHMA::pack_forward_comm(int n, int *list, double *buf,
+                                        int pbc_flag, int *pbc)
+{
+  double **xoriginal = fix->astore;
+  imageint *image = atom->image;
+  double **x = atom->x;
+  double *h = domain->h;
+  double xprd = domain->xprd;   
+  double yprd = domain->yprd;
+  double zprd = domain->zprd;
+
+  int m = 0;
+  for (int ii = 0; ii < n; ii++) {
+    int i = list[ii];
+    buf[m++] = deltaR[i][0];
+    buf[m++] = deltaR[i][1];
+    buf[m++] = deltaR[i][2];
+  }
+  return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeHMA::unpack_forward_comm(int n, int first, double *buf)
+{
+  double **xoriginal = fix->astore;
+  int i,m,last;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++) {
+    deltaR[i][0] = buf[m++];
+    deltaR[i][1] = buf[m++];
+    deltaR[i][2] = buf[m++];
+  }
+}
+
+
+/* ----------------------------------------------------------------------
+   initialize one atom's storage values, called when atom is created
+------------------------------------------------------------------------- */
+
+void ComputeHMA::set_arrays(int i)
+{
+  double **xoriginal = fix->astore;
+  double **x = atom->x;
+  xoriginal[i][0] = x[i][0];
+  xoriginal[i][1] = x[i][1];
+  xoriginal[i][2] = x[i][2];
+}
+
+double ComputeHMA::memory_usage()
+{
+  double bytes = nmax * 3 * sizeof(double);
+  return bytes;
+}
diff --git a/src/USER-MISC/compute_hma.h b/src/USER-MISC/compute_hma.h
new file mode 100644
index 0000000000..233e8bbe57
--- /dev/null
+++ b/src/USER-MISC/compute_hma.h
@@ -0,0 +1,67 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(hma,ComputeHMA)
+
+#else
+
+#ifndef LMP_COMPUTE_HMA_H
+#define LMP_COMPUTE_HMA_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeHMA : public Compute {
+ public:
+  ComputeHMA(class LAMMPS *, int, char **);
+  ~ComputeHMA();
+  void setup();
+  void init();
+  void init_list(int, class NeighList *);
+  void compute_vector();
+  void set_arrays(int);
+  int pack_forward_comm(int, int *, double *, int, int *);
+  void unpack_forward_comm(int, int, double *);
+  double memory_usage();
+
+ private:
+  int nmax;
+  int atomsingroup;
+  char *id_fix;
+  char *id_temp;
+  double finaltemp;
+  class FixStore *fix;
+  double boltz, nktv2p, inv_volume;
+  double deltaPcap;
+  double virial_compute(int);
+  static double sumVirial(int n, double* v) {
+    double x = 0;
+    for (int i=0; i<n; i++) x += v[i];
+    return x;
+  }
+  int computeU, computeP, computeCv;
+  class NeighList *list; // half neighbor list
+  double **deltaR;
+  int returnAnharmonic;
+  double uLat, pLat;
+};
+
+}
+
+#endif
+#endif
+
+ 
diff --git a/src/USER-MISC/compute_momentum.cpp b/src/USER-MISC/compute_momentum.cpp
new file mode 100644
index 0000000000..541b52d9c0
--- /dev/null
+++ b/src/USER-MISC/compute_momentum.cpp
@@ -0,0 +1,56 @@
+
+#include "compute_momentum.h"
+#include <mpi.h>
+#include "atom.h"
+#include "error.h"
+#include "update.h"
+
+using namespace LAMMPS_NS;
+
+ComputeMomentum::ComputeMomentum(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg)
+{
+  if (narg != 3) error->all(FLERR,"Illegal compute momentum command");
+
+  vector_flag = 1;
+  size_vector = 3;
+  extvector = 1;
+  vector = new double[size_vector];
+}
+
+ComputeMomentum::~ComputeMomentum() {
+  delete[] vector;
+}
+
+void ComputeMomentum::init()
+{
+}
+
+void ComputeMomentum::compute_vector()
+{
+  invoked_vector = update->ntimestep;
+
+  double **v = atom->v;
+  double *rmass = atom->rmass;
+  double *mass = atom->mass;
+  int *mask = atom->mask;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+
+  double mom[3] = {0.0, 0.0, 0.0};
+
+  if (rmass) {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        for(int j = 0; j < 3; ++j)
+          mom[j] += rmass[i] * v[i][j];
+      }
+  } else {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit)
+        for(int j = 0; j < 3; ++j)
+          mom[j] += mass[type[i]] * v[i][j];
+  }
+
+  MPI_Allreduce(&mom, vector, 3, MPI_DOUBLE, MPI_SUM, world);
+}
diff --git a/src/USER-MISC/compute_momentum.h b/src/USER-MISC/compute_momentum.h
new file mode 100644
index 0000000000..1e0c52c045
--- /dev/null
+++ b/src/USER-MISC/compute_momentum.h
@@ -0,0 +1,36 @@
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(momentum,ComputeMomentum)
+
+#else
+
+#ifndef LMP_COMPUTE_MOMENTUM_H
+#define LMP_COMPUTE_MOMENTUM_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeMomentum : public Compute {
+ public:
+  ComputeMomentum(class LAMMPS *, int, char **);
+  virtual ~ComputeMomentum();
+
+  virtual void init();
+  virtual void compute_vector();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+*/
diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp
index c250eaf677..6d2509d685 100644
--- a/src/USER-MISC/compute_pressure_cylinder.cpp
+++ b/src/USER-MISC/compute_pressure_cylinder.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
 #include "compute_pressure_cylinder.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
@@ -22,7 +21,6 @@
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "neigh_list.h"
-#include "group.h"
 #include "memory.h"
 #include "error.h"
 #include "citeme.h"
diff --git a/src/USER-MISC/compute_pressure_grem.cpp b/src/USER-MISC/compute_pressure_grem.cpp
index 087c01bd8e..ba949727b0 100644
--- a/src/USER-MISC/compute_pressure_grem.cpp
+++ b/src/USER-MISC/compute_pressure_grem.cpp
@@ -11,17 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
-#include <cstdlib>
 #include "compute_pressure_grem.h"
-#include "atom.h"
+#include <cstring>
 #include "update.h"
 #include "domain.h"
 #include "modify.h"
 #include "fix.h"
 #include "force.h"
-#include "pair.h"
 #include "kspace.h"
 #include "error.h"
 
diff --git a/src/USER-MISC/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp
index cb2a0b9713..2f932321e1 100644
--- a/src/USER-MISC/compute_stress_mop.cpp
+++ b/src/USER-MISC/compute_stress_mop.cpp
@@ -15,18 +15,14 @@
   Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
   --------------------------------------------------------------------------*/
 
+#include "compute_stress_mop.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
 
-#include "compute_stress_mop.h"
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
-#include "group.h"
-#include "modify.h"
-#include "fix.h"
 #include "neighbor.h"
 #include "force.h"
 #include "pair.h"
diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp
index 5499a37a46..5f6d0a36b2 100644
--- a/src/USER-MISC/compute_stress_mop_profile.cpp
+++ b/src/USER-MISC/compute_stress_mop_profile.cpp
@@ -15,18 +15,14 @@
   Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
   --------------------------------------------------------------------------*/
 
+#include "compute_stress_mop_profile.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
 
-#include "compute_stress_mop_profile.h"
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
-#include "group.h"
-#include "modify.h"
-#include "fix.h"
 #include "neighbor.h"
 #include "force.h"
 #include "pair.h"
diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/USER-MISC/compute_temp_rotate.cpp
index 36093bd1e1..94c6115186 100644
--- a/src/USER-MISC/compute_temp_rotate.cpp
+++ b/src/USER-MISC/compute_temp_rotate.cpp
@@ -15,16 +15,13 @@
    Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
-#include <cstring>
 #include "compute_temp_rotate.h"
+#include <mpi.h>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
 #include "group.h"
 #include "domain.h"
-#include "lattice.h"
 #include "error.h"
 #include "memory.h"
 
diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp
index c411ea8150..820dfabdeb 100644
--- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp
+++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp
@@ -15,14 +15,12 @@
    Contributing author: Carsten Svaneborg, science@zqex.dk
 ------------------------------------------------------------------------- */
 
+#include "dihedral_cosine_shift_exp.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "dihedral_cosine_shift_exp.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "memory.h"
diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.h b/src/USER-MISC/dihedral_cosine_shift_exp.h
index fc4be5049b..4d180f42de 100644
--- a/src/USER-MISC/dihedral_cosine_shift_exp.h
+++ b/src/USER-MISC/dihedral_cosine_shift_exp.h
@@ -20,7 +20,6 @@ DihedralStyle(cosine/shift/exp,DihedralCosineShiftExp)
 #ifndef LMP_DIHEDRAL_COSINE_SHIFT_EXP_H
 #define LMP_DIHEDRAL_COSINE_SHIFT_EXP_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp
index af86259c01..7cc250b1a8 100644
--- a/src/USER-MISC/dihedral_fourier.cpp
+++ b/src/USER-MISC/dihedral_fourier.cpp
@@ -16,16 +16,13 @@
    [ based on dihedral_charmm.cpp Paul Crozier (SNL) ]
 ------------------------------------------------------------------------- */
 
+#include "dihedral_fourier.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "dihedral_fourier.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
-#include "pair.h"
 #include "update.h"
 #include "math_const.h"
 #include "memory.h"
diff --git a/src/USER-MISC/dihedral_fourier.h b/src/USER-MISC/dihedral_fourier.h
index c1ed843c34..8b6291fc4c 100644
--- a/src/USER-MISC/dihedral_fourier.h
+++ b/src/USER-MISC/dihedral_fourier.h
@@ -20,7 +20,6 @@ DihedralStyle(fourier,DihedralFourier)
 #ifndef LMP_DIHEDRAL_FOURIER_H
 #define LMP_DIHEDRAL_FOURIER_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp
index ea2b76f415..f1e0018689 100644
--- a/src/USER-MISC/dihedral_nharmonic.cpp
+++ b/src/USER-MISC/dihedral_nharmonic.cpp
@@ -16,12 +16,11 @@
    [ based on dihedral_multi_harmonic.cpp Mathias Puetz (SNL) and friends ]
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "dihedral_nharmonic.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "update.h"
diff --git a/src/USER-MISC/dihedral_nharmonic.h b/src/USER-MISC/dihedral_nharmonic.h
index 7c6a35b200..6fd1da3b8b 100644
--- a/src/USER-MISC/dihedral_nharmonic.h
+++ b/src/USER-MISC/dihedral_nharmonic.h
@@ -20,7 +20,6 @@ DihedralStyle(nharmonic,DihedralNHarmonic)
 #ifndef DIHEDRAL_NHARMONIC_H
 #define DIHEDRAL_NHARMONIC_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp
index 8436e73c5c..02effc2f4f 100644
--- a/src/USER-MISC/dihedral_quadratic.cpp
+++ b/src/USER-MISC/dihedral_quadratic.cpp
@@ -16,12 +16,11 @@
    [ based on dihedral_helix.cpp Paul Crozier (SNL) ]
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "dihedral_quadratic.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "update.h"
diff --git a/src/USER-MISC/dihedral_quadratic.h b/src/USER-MISC/dihedral_quadratic.h
index edc29c3cf8..0b99cbc4f7 100644
--- a/src/USER-MISC/dihedral_quadratic.h
+++ b/src/USER-MISC/dihedral_quadratic.h
@@ -20,7 +20,6 @@ DihedralStyle(quadratic,DihedralQuadratic)
 #ifndef LMP_DIHEDRAL_QUADRATIC_H
 #define LMP_DIHEDRAL_QUADRATIC_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/USER-MISC/dihedral_spherical.cpp
index 3b30121551..78d45f923d 100644
--- a/src/USER-MISC/dihedral_spherical.cpp
+++ b/src/USER-MISC/dihedral_spherical.cpp
@@ -17,22 +17,19 @@
      and Paul Crozier (SNL) ]
 ------------------------------------------------------------------------- */
 
+#include "dihedral_spherical.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cassert>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "domain.h"
 #include "force.h"
-#include "pair.h"
-#include "update.h"
 #include "math_const.h"
 #include "math_extra.h"
 #include "memory.h"
 #include "error.h"
-#include "dihedral_spherical.h"
 
 using namespace std;
 using namespace LAMMPS_NS;
diff --git a/src/USER-MISC/dihedral_spherical.h b/src/USER-MISC/dihedral_spherical.h
index ae0ece189a..472db36f33 100644
--- a/src/USER-MISC/dihedral_spherical.h
+++ b/src/USER-MISC/dihedral_spherical.h
@@ -20,7 +20,6 @@ DihedralStyle(spherical,DihedralSpherical)
 #ifndef LMP_DIHEDRAL_SPHERICAL_H
 #define LMP_DIHEDRAL_SPHERICAL_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp
index ce5a32b603..59a16f376f 100644
--- a/src/USER-MISC/dihedral_table.cpp
+++ b/src/USER-MISC/dihedral_table.cpp
@@ -17,21 +17,20 @@
                           the "tridiag.c" written by Gerard Jungman for GSL
 ------------------------------------------------------------------------- */
 
+#include <mpi.h>
+#include <cctype>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include <cassert>
 #include <string>
-#include <fstream>
-#include <iostream>
-#include <sstream>
+#include <sstream>  // IWYU pragma: keep
+#include <fstream>  // IWYU pragma: keep
 
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "domain.h"
 #include "force.h"
-#include "update.h"
 #include "memory.h"
 #include "error.h"
 #include "dihedral_table.h"
diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp
index f5c85cc52b..87f0c9bf66 100644
--- a/src/USER-MISC/dihedral_table_cut.cpp
+++ b/src/USER-MISC/dihedral_table_cut.cpp
@@ -16,25 +16,23 @@
    Based on tabulated dihedral (dihedral_table.cpp) by Andrew Jewett
 ------------------------------------------------------------------------- */
 
+#include "dihedral_table_cut.h"
+#include <mpi.h>
+#include <cctype>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include <cassert>
 #include <string>
-#include <fstream>
-#include <iostream>
-#include <sstream>
+#include <fstream>  // IWYU pragma: keep
+#include <sstream>  // IWYU pragma: keep
 
-#include "dihedral_table_cut.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "update.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "citeme.h"
 #include "math_const.h"
-#include "math_extra.h"
 #include "memory.h"
 #include "error.h"
 #include "utils.h"
@@ -42,8 +40,6 @@
 using namespace LAMMPS_NS;
 using namespace MathConst;
 using namespace std;
-using namespace MathExtra;
-
 
 static const char cite_dihedral_tablecut[] =
   "dihedral_style  table/cut  command:\n\n"
diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp
index 2cd1ac7527..665f1d4a60 100644
--- a/src/USER-MISC/fix_addtorque.cpp
+++ b/src/USER-MISC/fix_addtorque.cpp
@@ -15,9 +15,9 @@
    Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "fix_addtorque.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
@@ -25,7 +25,6 @@
 #include "respa.h"
 #include "input.h"
 #include "variable.h"
-#include "memory.h"
 #include "error.h"
 #include "group.h"
 #include "force.h"
diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp
index dc52d94b14..b1bcc07fa7 100644
--- a/src/USER-MISC/fix_ave_correlate_long.cpp
+++ b/src/USER-MISC/fix_ave_correlate_long.cpp
@@ -21,11 +21,12 @@
    see J. Chem. Phys. 133, 154103 (2010)
 ------------------------------------------------------------------------- */
 
+#include "fix_ave_correlate_long.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
 #include <unistd.h>
-#include "fix_ave_correlate_long.h"
 #include "update.h"
 #include "modify.h"
 #include "compute.h"
diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/USER-MISC/fix_ave_correlate_long.h
index 548a0e7183..a0c5863e99 100644
--- a/src/USER-MISC/fix_ave_correlate_long.h
+++ b/src/USER-MISC/fix_ave_correlate_long.h
@@ -20,7 +20,6 @@ FixStyle(ave/correlate/long,FixAveCorrelateLong)
 #ifndef LMP_FIX_AVE_CORRELATE_LONG_H
 #define LMP_FIX_AVE_CORRELATE_LONG_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index c641912db6..05dc54c57e 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -15,11 +15,10 @@ See the README file in the top-level LAMMPS directory.
 Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
 ------------------------------------------------------------------------- */
 
+#include "fix_bond_react.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_bond_react.h"
 #include "update.h"
 #include "modify.h"
 #include "respa.h"
@@ -1286,7 +1285,7 @@ void FixBondReact::make_a_guess()
 
   for (int i = 0; i < nxspecial[atom->map(glove[pion][1])][0]; i++) {
     if (atom->map(xspecial[atom->map(glove[pion][1])][i]) < 0) {
-      error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away1"); // parallel issues.
+      error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); // parallel issues.
     }
     if (i_limit_tags[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] != 0) {
       status = GUESSFAIL;
@@ -1397,7 +1396,7 @@ void FixBondReact::check_a_neighbor()
 
             //another check for ghost atoms. perhaps remove the one in make_a_guess
             if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
-              error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away2");
+              error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away");
             }
 
             for (int j = 0; j < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; j++) {
@@ -1449,7 +1448,7 @@ void FixBondReact::check_a_neighbor()
 
         //another check for ghost atoms. perhaps remove the one in make_a_guess
         if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
-          error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away3");
+          error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away");
         }
 
         for (int ii = 0; ii < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; ii++) {
@@ -1560,7 +1559,7 @@ void FixBondReact::inner_crosscheck_loop()
 
   //another check for ghost atoms. perhaps remove the one in make_a_guess
   if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
-    error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away4");
+    error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away");
   }
 
   if (guess_branch[avail_guesses-1] == 0) avail_guesses--;
diff --git a/src/USER-MISC/fix_electron_stopping.cpp b/src/USER-MISC/fix_electron_stopping.cpp
index 0831ebcf89..2130f07420 100644
--- a/src/USER-MISC/fix_electron_stopping.cpp
+++ b/src/USER-MISC/fix_electron_stopping.cpp
@@ -16,16 +16,14 @@
    Information: k.avchachov@gmail.com
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_electron_stopping.h"
+#include <cmath>
+#include <cstring>
 #include "mpi.h"
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
 #include "region.h"
-#include "group.h"
 #include "force.h"
 #include "fix.h"
 #include "memory.h"
diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp
index 9ab113aeaa..a245b6b4e5 100644
--- a/src/USER-MISC/fix_ffl.cpp
+++ b/src/USER-MISC/fix_ffl.cpp
@@ -18,31 +18,21 @@
 
 /* ----------------------------------------------------------------------
    Contributing authors: Lionel Constantin (EPFL), David M. Wilkins (EPFL),
-			 Michele Ceriotti (EPFL)
+                         Michele Ceriotti (EPFL)
 ------------------------------------------------------------------------- */
 
+#include "fix_ffl.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_ffl.h"
-#include "math_extra.h"
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "force.h"
 #include "update.h"
-#include "modify.h"
-#include "compute.h"
-#include "domain.h"
-#include "region.h"
 #include "respa.h"
 #include "comm.h"
-#include "input.h"
-#include "variable.h"
 #include "random_mars.h"
 #include "memory.h"
 #include "error.h"
-#include "group.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp
index f6cc1c435f..bfc5f58f93 100644
--- a/src/USER-MISC/fix_filter_corotate.cpp
+++ b/src/USER-MISC/fix_filter_corotate.cpp
@@ -16,30 +16,25 @@
      some subroutines are from fix_shake.cpp
    ------------------------------------------------------------------------- */
 
+#include "fix_filter_corotate.h"
 #include <mpi.h>
+#include <cctype>
+#include <cmath>
 #include <cstring>
 #include <cstdlib>
-#include "fix_filter_corotate.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "molecule.h"
-#include "bond.h"
+#include "comm.h"
+#include "domain.h"
 #include "angle.h"
+#include "bond.h"
 #include "math_const.h"
 #include "update.h"
 #include "modify.h"
-#include "domain.h"
-#include "region.h"
 #include "memory.h"
 #include "error.h"
 #include "force.h"
-#include "comm.h"
-#include "error.h"
-#include "memory.h"
-#include "domain.h"
-#include "integrate.h"
 #include "respa.h"
-#include "neighbor.h"
 #include "citeme.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp
index b6366ec509..70be1f1e45 100644
--- a/src/USER-MISC/fix_flow_gauss.cpp
+++ b/src/USER-MISC/fix_flow_gauss.cpp
@@ -16,13 +16,12 @@
    Joel.Eaves@Colorado.edu
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_flow_gauss.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "group.h"
-#include "comm.h"
 #include "update.h"
 #include "domain.h"
 #include "error.h"
diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp
index 01da7f87cf..b8bdc66d08 100644
--- a/src/USER-MISC/fix_gle.cpp
+++ b/src/USER-MISC/fix_gle.cpp
@@ -16,28 +16,19 @@
                          Axel Kohylmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
+#include "fix_gle.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
 #include <cstdlib>
-#include "fix_gle.h"
-#include "math_extra.h"
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "force.h"
 #include "update.h"
-#include "modify.h"
-#include "compute.h"
-#include "domain.h"
-#include "region.h"
 #include "respa.h"
 #include "comm.h"
-#include "input.h"
-#include "variable.h"
 #include "random_mars.h"
 #include "memory.h"
 #include "error.h"
-#include "group.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-MISC/fix_grem.cpp b/src/USER-MISC/fix_grem.cpp
index 635acf705c..4272740068 100644
--- a/src/USER-MISC/fix_grem.cpp
+++ b/src/USER-MISC/fix_grem.cpp
@@ -22,19 +22,14 @@
                          Tom Keyes (Boston University)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
-#include "comm.h"
 #include "fix_grem.h"
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "modify.h"
 #include "domain.h"
-#include "input.h"
 #include "compute.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp
index 1c3eafdc46..10aaa285a5 100644
--- a/src/USER-MISC/fix_imd.cpp
+++ b/src/USER-MISC/fix_imd.cpp
@@ -58,8 +58,6 @@ negotiate an appropriate license for such distribution."
 #include "group.h"
 #include "memory.h"
 
-#include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 
diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp
index 32892d87a8..08b39ee89b 100644
--- a/src/USER-MISC/fix_ipi.cpp
+++ b/src/USER-MISC/fix_ipi.cpp
@@ -15,15 +15,12 @@
    Contributing author: Michele Ceriotti (EPFL), Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdio>
-#include <cstring>
-#include <cstdlib>
 #include "fix_ipi.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
-#include "respa.h"
 #include "error.h"
 #include "kspace.h"
 #include "modify.h"
@@ -32,8 +29,6 @@
 #include "neighbor.h"
 #include "irregular.h"
 #include "domain.h"
-#include "compute_pressure.h"
-#include <errno.h>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp
index 2ac2a7c9fc..410a269f8c 100644
--- a/src/USER-MISC/fix_nvk.cpp
+++ b/src/USER-MISC/fix_nvk.cpp
@@ -15,18 +15,16 @@
      Contributing author: Efrem Braun (UC Berkeley)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nvk.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "respa.h"
 #include "error.h"
-#include "compute.h"
 #include "math_extra.h"
-#include "domain.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp
index 3929d47d6b..8f790f0a59 100644
--- a/src/USER-MISC/fix_pimd.cpp
+++ b/src/USER-MISC/fix_pimd.cpp
@@ -21,10 +21,11 @@
    Version      1.0
 ------------------------------------------------------------------------- */
 
+#include "fix_pimd.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
 #include <cstdlib>
-#include "fix_pimd.h"
 #include "universe.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp
index 6a6e71ebaa..c638adf6a4 100644
--- a/src/USER-MISC/fix_rhok.cpp
+++ b/src/USER-MISC/fix_rhok.cpp
@@ -13,12 +13,11 @@
    Contributing author: Ulf R. Pedersen, ulf@urp.dk
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
+#include "fix_rhok.h"
+#include <mpi.h>
 #include <cstring>
 #include <cmath>
 
-#include "fix_rhok.h"
 #include "atom.h"
 #include "domain.h"
 #include "error.h"
diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp
index cbebdebdbf..32c040c2b4 100644
--- a/src/USER-MISC/fix_smd.cpp
+++ b/src/USER-MISC/fix_smd.cpp
@@ -16,10 +16,10 @@
    based on fix spring by: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_smd.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "update.h"
diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp
index ebc161ff99..c0db252db4 100644
--- a/src/USER-MISC/fix_srp.cpp
+++ b/src/USER-MISC/fix_srp.cpp
@@ -15,9 +15,10 @@
    Contributing authors: Timothy Sirk (ARL), Pieter in't Veld (BASF)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "fix_srp.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
@@ -635,11 +636,11 @@ void FixSRP::restart(char *buf)
 int FixSRP::modify_param(int /*narg*/, char **arg)
 {
   if (strcmp(arg[0],"btype") == 0) {
-    btype = atoi(arg[1]);
+    btype = force->inumeric(FLERR,arg[1]);
     return 2;
   }
   if (strcmp(arg[0],"bptype") == 0) {
-    bptype = atoi(arg[1]);
+    bptype = force->inumeric(FLERR,arg[1]);
     return 2;
   }
   return 0;
diff --git a/src/USER-MISC/fix_srp.h b/src/USER-MISC/fix_srp.h
index 7dbf044bda..f8343df8a6 100644
--- a/src/USER-MISC/fix_srp.h
+++ b/src/USER-MISC/fix_srp.h
@@ -20,7 +20,6 @@ FixStyle(SRP,FixSRP)
 #ifndef LMP_FIX_SRP_H
 #define LMP_FIX_SRP_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp
index 305e29e033..8481b34a6b 100644
--- a/src/USER-MISC/fix_ti_spring.cpp
+++ b/src/USER-MISC/fix_ti_spring.cpp
@@ -18,9 +18,9 @@
              Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_ti_spring.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp
index a34c2eb42f..55526a9149 100644
--- a/src/USER-MISC/fix_ttm_mod.cpp
+++ b/src/USER-MISC/fix_ttm_mod.cpp
@@ -17,17 +17,14 @@
    Vasily Pisarev (Joint Institute for High Temperatures of RAS)
 ------------------------------------------------------------------------- */
 
-#include "lmptype.h"
+#include "fix_ttm_mod.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_ttm_mod.h"
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "domain.h"
-#include "region.h"
 #include "respa.h"
 #include "comm.h"
 #include "random_mars.h"
diff --git a/src/USER-MISC/fix_wall_ees.cpp b/src/USER-MISC/fix_wall_ees.cpp
index 5ca16ebdad..bd7e230472 100644
--- a/src/USER-MISC/fix_wall_ees.cpp
+++ b/src/USER-MISC/fix_wall_ees.cpp
@@ -15,21 +15,13 @@
    Contributing author:  Abdoreza Ershadinia, a.ershadinia at gmail.com
 ------------------------------------------------------------------------- */
 
+#include "fix_wall_ees.h"
 #include <cmath>
 #include "math_extra.h"
-#include "fix_wall_ees.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "atom_vec_ellipsoid.h"
-#include "domain.h"
-#include "region.h"
-#include "force.h"
-#include "lattice.h"
-#include "update.h"
-#include "output.h"
-#include "respa.h"
 #include "error.h"
-#include "math_extra.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp
index 33bf636e64..5c6bb1874b 100644
--- a/src/USER-MISC/fix_wall_region_ees.cpp
+++ b/src/USER-MISC/fix_wall_region_ees.cpp
@@ -15,19 +15,16 @@
    Contributing author:  Abdoreza Ershadinia, a.ershadinia at gmail.com
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_wall_region_ees.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
 #include "atom_vec_ellipsoid.h"
 #include "domain.h"
 #include "region.h"
 #include "force.h"
-#include "lattice.h"
 #include "update.h"
-#include "output.h"
 #include "respa.h"
 #include "error.h"
 #include "math_extra.h"
diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp
index c8eb0808fb..2ea804b95d 100644
--- a/src/USER-MISC/improper_cossq.cpp
+++ b/src/USER-MISC/improper_cossq.cpp
@@ -16,14 +16,12 @@
      gvog@chemeng.ntua.gr
 ------------------------------------------------------------------------- */
 
+#include "improper_cossq.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "improper_cossq.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "memory.h"
diff --git a/src/USER-MISC/improper_cossq.h b/src/USER-MISC/improper_cossq.h
index ea880adfaf..9e430bfa1a 100644
--- a/src/USER-MISC/improper_cossq.h
+++ b/src/USER-MISC/improper_cossq.h
@@ -20,7 +20,6 @@ ImproperStyle(cossq,ImproperCossq)
 #ifndef LMP_IMPROPER_COSSQ_H
 #define LMP_IMPROPER_COSSQ_H
 
-#include <cstdio>
 #include "improper.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp
index 50babcc84e..2efab8b5f8 100644
--- a/src/USER-MISC/improper_distance.cpp
+++ b/src/USER-MISC/improper_distance.cpp
@@ -15,16 +15,14 @@
    Contributing author: Paolo Raiteri (Curtin University)
 ------------------------------------------------------------------------- */
 
+#include "improper_distance.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "improper_distance.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "domain.h"
 #include "force.h"
-#include "update.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-MISC/improper_distance.h b/src/USER-MISC/improper_distance.h
index 57e4d671e9..d7575c3585 100644
--- a/src/USER-MISC/improper_distance.h
+++ b/src/USER-MISC/improper_distance.h
@@ -20,7 +20,6 @@ ImproperStyle(distance,ImproperDistance)
 #ifndef LMP_IMPROPER_DISTANCE_H
 #define LMP_IMPROPER_DISTANCE_H
 
-#include <cstdio>
 #include "improper.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp
index 288d888d12..a0ef3a2058 100644
--- a/src/USER-MISC/improper_fourier.cpp
+++ b/src/USER-MISC/improper_fourier.cpp
@@ -16,15 +16,12 @@
    [ based on improper_umbrella.cpp Tod A Pascal (Caltech) ]
 ------------------------------------------------------------------------- */
 
+#include "improper_fourier.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include <cstring>
-#include "improper_fourier.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "memory.h"
diff --git a/src/USER-MISC/improper_fourier.h b/src/USER-MISC/improper_fourier.h
index 0525c45494..91dfacfd8e 100644
--- a/src/USER-MISC/improper_fourier.h
+++ b/src/USER-MISC/improper_fourier.h
@@ -20,7 +20,6 @@ ImproperStyle(fourier,ImproperFourier)
 #ifndef LMP_IMPROPER_FOURIER_H
 #define LMP_IMPROPER_FOURIER_H
 
-#include <cstdio>
 #include "improper.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp
index 36ba73af0f..48db5a41e9 100644
--- a/src/USER-MISC/improper_ring.cpp
+++ b/src/USER-MISC/improper_ring.cpp
@@ -36,16 +36,13 @@
                   of j.
 ------------------------------------------------------------------------- */
 
+#include "improper_ring.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include "improper_ring.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
-#include "update.h"
 #include "math_const.h"
 #include "math_special.h"
 #include "memory.h"
diff --git a/src/USER-MISC/improper_ring.h b/src/USER-MISC/improper_ring.h
index c31329816f..7c53c6f59f 100644
--- a/src/USER-MISC/improper_ring.h
+++ b/src/USER-MISC/improper_ring.h
@@ -20,7 +20,6 @@ ImproperStyle(ring,ImproperRing)
 #ifndef LMP_IMPROPER_RING_H
 #define LMP_IMPROPER_RING_H
 
-#include <cstdio>
 #include "improper.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp
index 21a6f1deee..b3abc647ef 100644
--- a/src/USER-MISC/pair_agni.cpp
+++ b/src/USER-MISC/pair_agni.cpp
@@ -15,18 +15,16 @@
    Contributing authors: Axel Kohlmeyer (Temple U), Venkatesh Botu
 ------------------------------------------------------------------------- */
 
+#include "pair_agni.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_agni.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "force.h"
 #include "comm.h"
-#include "memory.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp
index afd15d7fdb..e977197522 100644
--- a/src/USER-MISC/pair_buck_mdf.cpp
+++ b/src/USER-MISC/pair_buck_mdf.cpp
@@ -15,21 +15,18 @@
    Contributing author: Paolo Raiteri (Curtin University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_buck_mdf.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neigh_list.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp
new file mode 100644
index 0000000000..4544a6db43
--- /dev/null
+++ b/src/USER-MISC/pair_cosine_squared.cpp
@@ -0,0 +1,487 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing authors: Eugen Rozic (University College London)
+------------------------------------------------------------------------- */
+
+#include "pair_cosine_squared.h"
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "update.h"
+#include "integrate.h"
+#include "respa.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+/* ---------------------------------------------------------------------- */
+
+PairCosineSquared::PairCosineSquared(LAMMPS *lmp) : Pair(lmp)
+{
+  writedata = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairCosineSquared::~PairCosineSquared()
+{
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(epsilon);
+    memory->destroy(sigma);
+    memory->destroy(w);
+    memory->destroy(cut);
+    memory->destroy(wcaflag);
+
+    memory->destroy(lj12_e);
+    memory->destroy(lj6_e);
+    memory->destroy(lj12_f);
+    memory->destroy(lj6_f);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairCosineSquared::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes;
+  memory->create(setflag, n+1, n+1, "pair:setflag");
+  memory->create(cutsq, n+1, n+1, "pair:cutsq");
+
+  memory->create(cut, n+1, n+1, "pair:cut");
+  memory->create(epsilon, n+1, n+1, "pair:epsilon");
+  memory->create(sigma, n+1, n+1, "pair:sigma");
+  memory->create(w, n+1, n+1, "pair:w");
+  memory->create(wcaflag, n+1, n+1, "pair:wcaflag");
+
+  memory->create(lj12_e, n+1, n+1, "pair:lj12_e");
+  memory->create(lj6_e, n+1, n+1, "pair:lj6_e");
+  memory->create(lj12_f, n+1, n+1, "pair:lj12_f");
+  memory->create(lj6_f, n+1, n+1, "pair:lj6_f");
+
+  for (int i = 1; i <= n; i++) {
+    for (int j = i; j <= n; j++) {
+      setflag[i][j] = 0;
+      wcaflag[i][j] = 0;
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairCosineSquared::settings(int narg, char **arg)
+{
+  if (narg != 1) {
+    error->all(FLERR, "Illegal pair_style command (wrong number of params)");
+  }
+
+  cut_global = force->numeric(FLERR, arg[0]);
+
+  // reset cutoffs that have been explicitly set
+
+  if (allocated) {
+    int i, j;
+    for (i = 1; i <= atom->ntypes; i++)
+      for (j = i+1; j <= atom->ntypes; j++)
+        if (setflag[i][j])
+          cut[i][j] = cut_global;
+  }
+}
+
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairCosineSquared::coeff(int narg, char **arg)
+{
+  if (narg < 4 || narg > 6)
+    error->all(FLERR, "Incorrect args for pair coefficients (too few or too many)");
+  
+  if (!allocated)
+    allocate();
+
+  int ilo, ihi, jlo, jhi;
+  force->bounds(FLERR, arg[0], atom->ntypes, ilo, ihi);
+  force->bounds(FLERR, arg[1], atom->ntypes, jlo, jhi);
+
+  double epsilon_one = force->numeric(FLERR, arg[2]);
+  double sigma_one = force->numeric(FLERR, arg[3]);
+
+  double cut_one = cut_global;
+  double wca_one = 0;
+  if (narg == 6) {
+    cut_one = force->numeric(FLERR, arg[4]);
+    if (strcmp(arg[5], "wca") == 0) {
+      wca_one = 1;
+    } else {
+      error->all(FLERR, "Incorrect args for pair coefficients (unknown option)");
+    }
+  } else if (narg == 5) {
+    if (strcmp(arg[4], "wca") == 0) {
+      wca_one = 1;
+    } else {
+      cut_one = force->numeric(FLERR, arg[4]);
+    }
+  }
+
+  if (cut_one < sigma_one) {
+    error->all(FLERR, "Incorrect args for pair coefficients (cutoff < sigma)");
+  } else if (cut_one == sigma_one) {
+    if (wca_one == 0) {
+      error->all(FLERR, "Incorrect args for pair coefficients (cutoff = sigma w/o wca)");
+    } else {
+      error->warning(FLERR, "Cosine/squared set to WCA only (cutoff = sigma)");
+    }
+  }
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo,i); j <= jhi; j++) {
+      epsilon[i][j] = epsilon_one;
+      sigma[i][j] = sigma_one;
+      cut[i][j] = cut_one;
+      wcaflag[i][j] = wca_one;
+      setflag[i][j] = 1;
+      count++;
+    }
+  }
+
+  if (count == 0)
+    error->all(FLERR, "Incorrect args for pair coefficients (none set)");
+}
+
+/* ----------------------------------------------------------------------
+   init specific to this pair style (unneccesary)
+------------------------------------------------------------------------- */
+
+/*
+void PairCosineSquared::init_style()
+{
+  neighbor->request(this,instance_me);
+}
+*/
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairCosineSquared::init_one(int i, int j)
+{
+  if (setflag[i][j] == 0)
+    error->all(FLERR, "Mixing not supported in pair_style cosine/squared");
+
+  epsilon[j][i] = epsilon[i][j];
+  sigma[j][i] = sigma[i][j];
+  cut[j][i] = cut[i][j];
+  wcaflag[j][i] = wcaflag[i][j];
+
+  w[j][i] = w[i][j] = cut[i][j] - sigma[i][j];
+
+  if (wcaflag[i][j]) {
+    lj12_e[j][i] = lj12_e[i][j] = epsilon[i][j] * pow(sigma[i][j], 12.0);
+    lj6_e[j][i] = lj6_e[i][j] = 2.0 * epsilon[i][j] * pow(sigma[i][j], 6.0);
+    lj12_f[j][i] = lj12_f[i][j] = 12.0 * epsilon[i][j] * pow(sigma[i][j], 12.0);
+    lj6_f[j][i] = lj6_f[i][j] = 12.0 * epsilon[i][j] * pow(sigma[i][j], 6.0);
+  }
+
+  // Note: cutsq is set in pair.cpp
+
+  return cut[i][j];
+}
+
+/* ----------------------------------------------------------------------
+   this is here to throw errors & warnings for given options
+------------------------------------------------------------------------- */
+
+void PairCosineSquared::modify_params(int narg, char **arg)
+{
+  Pair::modify_params(narg, arg);
+
+  int iarg = 0;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg], "mix") == 0) {
+      error->all(FLERR, "pair_modify mix not supported for pair_style cosine/squared");
+    } else if (strcmp(arg[iarg], "shift") == 0) {
+      error->warning(FLERR, "pair_modify shift has no effect on pair_style cosine/squared");
+      offset_flag = 0;
+    } else if (strcmp(arg[iarg], "tail") == 0) {
+      error->warning(FLERR, "pair_modify tail has no effect on pair_style cosine/squared");
+      tail_flag = 0;
+    }
+    iarg++;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairCosineSquared::write_restart(FILE *fp)
+{
+  write_restart_settings(fp);
+
+  int i, j;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      fwrite(&setflag[i][j], sizeof(int), 1, fp);
+      if (setflag[i][j]) {
+        fwrite(&epsilon[i][j], sizeof(double), 1, fp);
+        fwrite(&sigma[i][j], sizeof(double), 1, fp);
+        fwrite(&cut[i][j], sizeof(double), 1, fp);
+        fwrite(&wcaflag[i][j], sizeof(int), 1, fp);
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairCosineSquared::read_restart(FILE *fp)
+{
+  read_restart_settings(fp);
+  allocate();
+
+  int i,j;
+  int me = comm->me;
+  for (i = 1; i <= atom->ntypes; i++) {
+    for (j = i; j <= atom->ntypes; j++) {
+      if (me == 0)
+        fread(&setflag[i][j], sizeof(int), 1, fp);
+      MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
+      if (setflag[i][j]) {
+        if (me == 0) {
+          fread(&epsilon[i][j], sizeof(double), 1, fp);
+          fread(&sigma[i][j], sizeof(double), 1, fp);
+          fread(&cut[i][j], sizeof(double), 1, fp);
+          fread(&wcaflag[i][j], sizeof(int), 1, fp);
+        }
+        MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world);
+        MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world);
+        MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
+        MPI_Bcast(&wcaflag[i][j], 1, MPI_INT, 0, world);
+      }
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairCosineSquared::write_restart_settings(FILE *fp)
+{
+  fwrite(&cut_global, sizeof(double), 1, fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairCosineSquared::read_restart_settings(FILE *fp)
+{
+  int me = comm->me;
+  if (me == 0) {
+    fread(&cut_global, sizeof(double), 1, fp);
+  }
+  MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairCosineSquared::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp, "%d %g %g %g %d\n", i, epsilon[i][i], sigma[i][i],
+            cut[i][i], wcaflag[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairCosineSquared::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp, "%d %d %g %g %g %d\n", i, j, epsilon[i][j], sigma[i][j],
+              cut[i][j], wcaflag[i][j]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairCosineSquared::compute(int eflag, int vflag)
+{
+  int i, j, ii, jj, inum, jnum, itype, jtype;
+  int *ilist, *jlist, *numneigh, **firstneigh;
+  double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
+  double r, rsq, r2inv, r6inv;
+  double factor_lj, force_lj, force_cos, cosone;
+
+  evdwl = 0.0;
+  if (eflag || vflag)
+    ev_setup(eflag, vflag);
+  else
+    evflag = vflag_fdotr = 0;
+
+  double **x = atom->x;
+  double **f = atom->f;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+  double *special_lj = force->special_lj;
+  int newton_pair = force->newton_pair;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // loop over neighbors of my atoms
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    itype = type[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      factor_lj = special_lj[sbmask(j)];
+      j &= NEIGHMASK;
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+      jtype = type[j];
+
+      if (rsq < cutsq[itype][jtype]) {
+
+        /*
+          This is exactly what the "single" method does, in fact it could be called
+          here instead of repeating the code but here energy calculation is optional
+          so a little bit of calculation is possibly saved
+        */
+
+        r = sqrt(rsq);
+
+        if (r <= sigma[itype][jtype]) {
+          if (wcaflag[itype][jtype]) {
+            r2inv = 1.0/rsq;
+            r6inv = r2inv*r2inv*r2inv;
+            force_lj = r6inv*(lj12_f[itype][jtype]*r6inv - lj6_f[itype][jtype]);
+            fpair = factor_lj*force_lj*r2inv;
+            if (eflag) {
+              evdwl = factor_lj*r6inv*
+                      (lj12_e[itype][jtype]*r6inv - lj6_e[itype][jtype]);
+              if (sigma[itype][jtype] == cut[itype][jtype]) {
+                // this is the WCA-only case (it requires this shift by definition)
+                evdwl += factor_lj*epsilon[itype][jtype];
+              }
+            }
+          } else {
+            fpair = 0.0;
+            if (eflag) {
+              evdwl = -factor_lj*epsilon[itype][jtype];
+            }
+          }
+        } else {
+          force_cos = -(MY_PI*epsilon[itype][jtype] / (2.0*w[itype][jtype])) *
+                      sin(MY_PI*(r-sigma[itype][jtype]) / w[itype][jtype]);
+          fpair = factor_lj*force_cos / r;
+          if (eflag) {
+            cosone = cos(MY_PI*(r-sigma[itype][jtype]) / (2.0*w[itype][jtype]));
+            evdwl = -factor_lj*epsilon[itype][jtype]*cosone*cosone;
+          }
+        }
+
+        f[i][0] += delx*fpair;
+        f[i][1] += dely*fpair;
+        f[i][2] += delz*fpair;
+
+        if (newton_pair || j < nlocal) {
+          f[j][0] -= delx*fpair;
+          f[j][1] -= dely*fpair;
+          f[j][2] -= delz*fpair;
+        }
+
+        if (evflag)
+          ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
+      }
+    }
+  }
+
+  if (vflag_fdotr)
+    virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+   This is used be pair_write;
+   it is called only if rsq < cutsq[itype][jtype], no need to check that
+------------------------------------------------------------------------- */
+
+double PairCosineSquared::single(int /* i */, int /* j */, int itype, int jtype, double rsq,
+                         double /* factor_coul */, double factor_lj,
+                         double &fforce)
+{
+  double r, r2inv, r6inv, cosone, force, energy;
+  
+  r = sqrt(rsq);
+
+  if (r <= sigma[itype][jtype]) {
+    if (wcaflag[itype][jtype]) {
+      r2inv = 1.0/rsq;
+      r6inv = r2inv*r2inv*r2inv;
+      force = r6inv*(lj12_f[itype][jtype]*r6inv - lj6_f[itype][jtype])*r2inv;
+      energy = r6inv*(lj12_e[itype][jtype]*r6inv - lj6_e[itype][jtype]);
+      if (sigma[itype][jtype] == cut[itype][jtype]) {
+        // this is the WCA-only case (it requires this shift by definition)
+        energy += epsilon[itype][jtype];
+      }
+    } else {
+      force = 0.0;
+      energy = -epsilon[itype][jtype];
+    }
+  } else {
+    cosone = cos(MY_PI*(r-sigma[itype][jtype]) / (2.0*w[itype][jtype]));
+    force = -(MY_PI*epsilon[itype][jtype] / (2.0*w[itype][jtype])) * 
+                 sin(MY_PI*(r-sigma[itype][jtype]) / w[itype][jtype]) / r;
+    energy = -epsilon[itype][jtype]*cosone*cosone;
+  }
+  fforce = factor_lj*force;
+  return factor_lj*energy;
+}
+
diff --git a/src/USER-MISC/pair_cosine_squared.h b/src/USER-MISC/pair_cosine_squared.h
new file mode 100644
index 0000000000..a638270e68
--- /dev/null
+++ b/src/USER-MISC/pair_cosine_squared.h
@@ -0,0 +1,100 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing authors: Eugen Rozic (University College London)
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(cosine/squared, PairCosineSquared)
+
+#else
+
+#ifndef LMP_PAIR_LJ_COS_SQ_H
+#define LMP_PAIR_LJ_COS_SQ_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairCosineSquared : public Pair {
+ public:
+  PairCosineSquared(class LAMMPS *);
+  virtual ~PairCosineSquared();
+  void settings(int, char **);
+  void coeff(int, char **);
+  // void init_style();
+  double init_one(int, int);
+  void modify_params(int, char **);
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_restart_settings(FILE *);
+  void read_restart_settings(FILE *);
+  void write_data(FILE *);
+  void write_data_all(FILE *);
+  virtual void compute(int, int);
+  double single(int, int, int, int, double, double, double, double &);
+  // void *extract(const char *, int &);
+
+/* RESPA stuff not implemented...
+  void compute_inner();
+  void compute_middle();
+  void compute_outer(int, int);
+*/
+
+ protected:
+  double cut_global;
+  double **epsilon, **sigma, **w, **cut;
+  int **wcaflag;
+  double **lj12_e, **lj6_e, **lj12_f, **lj6_f;
+
+  virtual void allocate();
+};
+
+}  // namespace LAMMPS_NS
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+E: Mixing not supported in pair_style cosine/squared
+
+Self-explanatory. All coefficients need to be specified explicitly.
+
+E: pair_modify mix not supported for pair_style cosine/squared
+
+Same as above, only when calling "pair_modify" command
+
+W: pair_modify shift/tail is meaningless for pair_style cosine/squared
+
+This style by definition gets to zero at cutoff distance, so there is nothing
+to shift and there is no tail contribution
+
+W: Cosine/squared set to WCA only (cutoff = sigma)
+
+If cutoff is equal to sigma (minimum) then this pair style basically
+degenerates/reverts to only WCA. This is for convenience.
+
+*/
+
diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp
index a86921d296..a375901ecd 100644
--- a/src/USER-MISC/pair_coul_diel.cpp
+++ b/src/USER-MISC/pair_coul_diel.cpp
@@ -14,11 +14,9 @@
    Contributiong authors: Arben Jusufi, Axel Kohlmeyer (Temple U.)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_diel.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp
index f74dcfe7d8..9264e51287 100644
--- a/src/USER-MISC/pair_coul_shield.cpp
+++ b/src/USER-MISC/pair_coul_shield.cpp
@@ -18,11 +18,8 @@
    [Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017)]
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_shield.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_drip.cpp b/src/USER-MISC/pair_drip.cpp
index 118c033b5c..20ec3abcf9 100644
--- a/src/USER-MISC/pair_drip.cpp
+++ b/src/USER-MISC/pair_drip.cpp
@@ -20,19 +20,17 @@
    Phys. Rev. B, 98, 235404 (2018).
 ------------------------------------------------------------------------- */
 
+#include "pair_drip.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include <mpi.h>
-#include "pair_drip.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "my_page.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-MISC/pair_drip.h b/src/USER-MISC/pair_drip.h
index 0a8f90dfc2..3ea6c735a6 100644
--- a/src/USER-MISC/pair_drip.h
+++ b/src/USER-MISC/pair_drip.h
@@ -31,8 +31,6 @@ PairStyle(drip, PairDRIP)
 #define LMP_PAIR_DRIP_H
 
 #include "pair.h"
-#include "my_page.h"
-#include <cmath>
 
 namespace LAMMPS_NS {
 
diff --git a/src/USER-MISC/pair_e3b.cpp b/src/USER-MISC/pair_e3b.cpp
index 43b472594a..aa19849baa 100644
--- a/src/USER-MISC/pair_e3b.cpp
+++ b/src/USER-MISC/pair_e3b.cpp
@@ -14,16 +14,14 @@
    contact: stevene.strong at gmail dot com
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-
 #include "pair_e3b.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <algorithm>
 
 #include "atom.h"
 #include "neighbor.h"
-#include "neigh_request.h"
 #include "neigh_list.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp
index 0b5220fdfd..8dee4a606b 100644
--- a/src/USER-MISC/pair_edip.cpp
+++ b/src/USER-MISC/pair_edip.cpp
@@ -21,12 +21,12 @@
        Phys. Rev. B 58, 2539 (1998)
 ------------------------------------------------------------------------- */
 
+#include "pair_edip.h"
+#include <mpi.h>
 #include <cmath>
 #include <cfloat>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_edip.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp
index ab48fbaa73..9f953610de 100644
--- a/src/USER-MISC/pair_edip_multi.cpp
+++ b/src/USER-MISC/pair_edip_multi.cpp
@@ -17,12 +17,11 @@
    Contributing author: Chao Jiang
 ------------------------------------------------------------------------- */
 
+#include "pair_edip_multi.h"
+#include <mpi.h>
 #include <cmath>
-#include <cfloat>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_edip_multi.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp
index bd5da71f4a..8507fd49f6 100644
--- a/src/USER-MISC/pair_extep.cpp
+++ b/src/USER-MISC/pair_extep.cpp
@@ -15,12 +15,12 @@
    Contributing author: Jan Los
 ------------------------------------------------------------------------- */
 
+#include "pair_extep.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 #include <cctype>
-#include "pair_extep.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-MISC/pair_extep.h b/src/USER-MISC/pair_extep.h
index 535e7261e3..1f127b71e0 100644
--- a/src/USER-MISC/pair_extep.h
+++ b/src/USER-MISC/pair_extep.h
@@ -21,7 +21,6 @@ PairStyle(extep,PairExTeP)
 #define LMP_PAIR_EXTEP_H
 
 #include "pair.h"
-#include "my_page.h"
 
 #define MAXTYPES 8
 #define NSPLINE 5
diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp
index 24d0b191d8..e6cfc02f63 100644
--- a/src/USER-MISC/pair_gauss_cut.cpp
+++ b/src/USER-MISC/pair_gauss_cut.cpp
@@ -15,18 +15,13 @@
    Contributing authors: Arben Jusufi, Axel Kohlmeyer (Temple U.)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_gauss_cut.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "update.h"
-#include "integrate.h"
 #include "memory.h"
 #include "error.h"
 #include "math_const.h"
diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
index a41c660b7b..4741263603 100644
--- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp
+++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
@@ -20,12 +20,11 @@
    [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)]
 ------------------------------------------------------------------------- */
 
+#include "pair_ilp_graphene_hbn.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_ilp_graphene_hbn.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -49,6 +48,9 @@ PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp)
   restartinfo = 0;
   one_coeff = 1;
 
+  nextra = 2;
+  pvector = new double[nextra];
+
   // initialize element to parameter maps
   nelements = 0;
   elements = NULL;
@@ -71,9 +73,7 @@ PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp)
 
   // always compute energy offset
   offset_flag = 1;
-
-  // set comm size needed by this pair style
-  comm_forward = 39;
+  // turn on the taper function
   tap_flag = 1;
 }
 
@@ -84,6 +84,7 @@ PairILPGrapheneHBN::~PairILPGrapheneHBN()
   memory->destroy(ILP_numneigh);
   memory->sfree(ILP_firstneigh);
   delete [] ipage;
+  delete [] pvector;
   memory->destroy(normal);
   memory->destroy(dnormal);
   memory->destroy(dnormdri);
@@ -104,649 +105,6 @@ PairILPGrapheneHBN::~PairILPGrapheneHBN()
   if (allocated) delete [] map;
 }
 
-/* ---------------------------------------------------------------------- */
-
-void PairILPGrapheneHBN::compute(int eflag, int vflag)
-{
-  int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll;
-  tagint itag,jtag;
-  double prodnorm1,prodnorm2,fkcx,fkcy,fkcz;
-  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1,fpair2;
-  double rsq,r,Rcut,rhosq1,rhosq2,exp0,exp1,exp2,r2inv,r6inv,r8inv,Tap,dTap,Vilp;
-  double frho1,frho2,TSvdw,TSvdw2inv,Erep,fsum,rdsq1,rdsq2;
-  int *ilist,*jlist,*numneigh,**firstneigh;
-  int *ILP_neighs_i,*ILP_neighs_j;
-
-  evdwl = 0.0;
-  ev_init(eflag,vflag);
-
-  double **x = atom->x;
-  double **f = atom->f;
-  int *type = atom->type;
-  tagint *tag = atom->tag;
-  int nlocal = atom->nlocal;
-  int newton_pair = force->newton_pair;
-  double dprodnorm1[3] = {0.0, 0.0, 0.0};
-  double dprodnorm2[3] = {0.0, 0.0, 0.0};
-  double fp1[3] = {0.0, 0.0, 0.0};
-  double fp2[3] = {0.0, 0.0, 0.0};
-  double fprod1[3] = {0.0, 0.0, 0.0};
-  double fprod2[3] = {0.0, 0.0, 0.0};
-  double fk[3] = {0.0, 0.0, 0.0};
-  double fl[3] = {0.0, 0.0, 0.0};
-  double delkj[3] = {0.0, 0.0, 0.0};
-  double delli[3] = {0.0, 0.0, 0.0};
-
-  inum = list->inum;
-  ilist = list->ilist;
-  numneigh = list->numneigh;
-  firstneigh = list->firstneigh;
-  // Build full neighbor list
-  ILP_neigh();
-  // Calculate the normals
-  calc_normal();
-
-  // communicate the normal vector and its derivatives
-  comm->forward_comm_pair(this);
-
-  // loop over neighbors of my atoms
-  for (ii = 0; ii < inum; ii++) {
-    i = ilist[ii];
-    itag = tag[i];
-    xtmp = x[i][0];
-    ytmp = x[i][1];
-    ztmp = x[i][2];
-    itype = type[i];
-    jlist = firstneigh[i];
-    jnum = numneigh[i];
-
-    for (jj = 0; jj < jnum; jj++) {
-      j = jlist[jj];
-      j &= NEIGHMASK;
-      jtype = type[j];
-      jtag = tag[j];
-
-      // two-body interactions from full neighbor list, skip half of them
-      if (itag > jtag) {
-        if ((itag+jtag) % 2 == 0) continue;
-      } else if (itag < jtag) {
-        if ((itag+jtag) % 2 == 1) continue;
-      } else {
-        if (x[j][2] < ztmp) continue;
-        if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
-        if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
-      }
-
-      delx = xtmp - x[j][0];
-      dely = ytmp - x[j][1];
-      delz = ztmp - x[j][2];
-      rsq = delx*delx + dely*dely + delz*delz;
-
-      // only include the interation between different layers
-      if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) {
-
-        int iparam_ij = elem2param[map[itype]][map[jtype]];
-        Param& p = params[iparam_ij];
-
-        r = sqrt(rsq);
-        r2inv = 1.0/rsq;
-        r6inv = r2inv*r2inv*r2inv;
-        r8inv = r6inv*r2inv;
-        // turn on/off taper function
-        if (tap_flag) {
-          Rcut = sqrt(cutsq[itype][jtype]);
-          Tap = calc_Tap(r,Rcut);
-          dTap = calc_dTap(r,Rcut);
-        } else {Tap = 1.0; dTap = 0.0;}
-
-        // Calculate the transverse distance
-        // note that rho_ij does not equal to rho_ji except when normals are all along z
-        prodnorm1 = normal[i][0]*delx + normal[i][1]*dely + normal[i][2]*delz;
-        prodnorm2 = normal[j][0]*delx + normal[j][1]*dely + normal[j][2]*delz;
-        rhosq1 = rsq - prodnorm1*prodnorm1;  // rho_ij
-        rhosq2 = rsq - prodnorm2*prodnorm2;  // rho_ji
-        rdsq1 = rhosq1*p.delta2inv; // (rho_ij/delta)^2
-        rdsq2 = rhosq2*p.delta2inv; // (rho_ji/delta)^2
-
-        // store exponents
-        exp0 = exp(-p.lambda*(r-p.z0));
-        exp1 = exp(-rdsq1);
-        exp2 = exp(-rdsq2);
-
-        TSvdw = 1.0 + exp(-p.d*(r/p.seff - 1.0));
-        TSvdw2inv = 1.0/pow(TSvdw,2.0);
-        frho1 = exp1*p.C;
-        frho2 = exp2*p.C;
-        Erep = p.epsilon + frho1 + frho2;
-        Vilp = -p.C6*r6inv/TSvdw + exp0*Erep;
-
-        // derivatives
-        fpair = -6.0*p.C6*r8inv/TSvdw + p.d/p.seff*p.C6*(TSvdw-1.0)*TSvdw2inv*r8inv*r + p.lambda*exp0/r*Erep;
-        fpair1 = 2.0*exp0*frho1*p.delta2inv;
-        fpair2 = 2.0*exp0*frho2*p.delta2inv;
-        fsum = fpair + fpair1 + fpair2;
-        // derivatives of the product of rij and ni, the result is a vector
-        dprodnorm1[0] = dnormdri[0][0][i]*delx + dnormdri[1][0][i]*dely + dnormdri[2][0][i]*delz;
-        dprodnorm1[1] = dnormdri[0][1][i]*delx + dnormdri[1][1][i]*dely + dnormdri[2][1][i]*delz;
-        dprodnorm1[2] = dnormdri[0][2][i]*delx + dnormdri[1][2][i]*dely + dnormdri[2][2][i]*delz;
-        // derivatives of the product of rji and nj, the result is a vector
-        dprodnorm2[0] = dnormdri[0][0][j]*delx + dnormdri[1][0][j]*dely + dnormdri[2][0][j]*delz;
-        dprodnorm2[1] = dnormdri[0][1][j]*delx + dnormdri[1][1][j]*dely + dnormdri[2][1][j]*delz;
-        dprodnorm2[2] = dnormdri[0][2][j]*delx + dnormdri[1][2][j]*dely + dnormdri[2][2][j]*delz;
-        fp1[0] = prodnorm1*normal[i][0]*fpair1;
-        fp1[1] = prodnorm1*normal[i][1]*fpair1;
-        fp1[2] = prodnorm1*normal[i][2]*fpair1;
-        fp2[0] = prodnorm2*normal[j][0]*fpair2;
-        fp2[1] = prodnorm2*normal[j][1]*fpair2;
-        fp2[2] = prodnorm2*normal[j][2]*fpair2;
-        fprod1[0] = prodnorm1*dprodnorm1[0]*fpair1;
-        fprod1[1] = prodnorm1*dprodnorm1[1]*fpair1;
-        fprod1[2] = prodnorm1*dprodnorm1[2]*fpair1;
-        fprod2[0] = prodnorm2*dprodnorm2[0]*fpair2;
-        fprod2[1] = prodnorm2*dprodnorm2[1]*fpair2;
-        fprod2[2] = prodnorm2*dprodnorm2[2]*fpair2;
-        fkcx = (delx*fsum - fp1[0] - fp2[0])*Tap - Vilp*dTap*delx/r;
-        fkcy = (dely*fsum - fp1[1] - fp2[1])*Tap - Vilp*dTap*dely/r;
-        fkcz = (delz*fsum - fp1[2] - fp2[2])*Tap - Vilp*dTap*delz/r;
-
-        f[i][0] += fkcx - fprod1[0]*Tap;
-        f[i][1] += fkcy - fprod1[1]*Tap;
-        f[i][2] += fkcz - fprod1[2]*Tap;
-        f[j][0] -= fkcx + fprod2[0]*Tap;
-        f[j][1] -= fkcy + fprod2[1]*Tap;
-        f[j][2] -= fkcz + fprod2[2]*Tap;
-
-        // calculate the forces acted on the neighbors of atom i from atom j
-        ILP_neighs_i = ILP_firstneigh[i];
-        for (kk = 0; kk < ILP_numneigh[i]; kk++) {
-          k = ILP_neighs_i[kk];
-          if (k == i) continue;
-          // derivatives of the product of rij and ni respect to rk, k=0,1,2, where atom k is the neighbors of atom i
-          dprodnorm1[0] = dnormal[0][0][kk][i]*delx + dnormal[1][0][kk][i]*dely + dnormal[2][0][kk][i]*delz;
-          dprodnorm1[1] = dnormal[0][1][kk][i]*delx + dnormal[1][1][kk][i]*dely + dnormal[2][1][kk][i]*delz;
-          dprodnorm1[2] = dnormal[0][2][kk][i]*delx + dnormal[1][2][kk][i]*dely + dnormal[2][2][kk][i]*delz;
-          fk[0] = (-prodnorm1*dprodnorm1[0]*fpair1)*Tap;
-          fk[1] = (-prodnorm1*dprodnorm1[1]*fpair1)*Tap;
-          fk[2] = (-prodnorm1*dprodnorm1[2]*fpair1)*Tap;
-          f[k][0] += fk[0];
-          f[k][1] += fk[1];
-          f[k][2] += fk[2];
-          delkj[0] = x[k][0] - x[j][0];
-          delkj[1] = x[k][1] - x[j][1];
-          delkj[2] = x[k][2] - x[j][2];
-          if (evflag) ev_tally_xyz(k,j,nlocal,newton_pair,0.0,0.0,fk[0],fk[1],fk[2],delkj[0],delkj[1],delkj[2]);
-        }
-
-        // calculate the forces acted on the neighbors of atom j from atom i
-        ILP_neighs_j = ILP_firstneigh[j];
-        for (ll = 0; ll < ILP_numneigh[j]; ll++) {
-          l = ILP_neighs_j[ll];
-          if (l == j) continue;
-          // derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j
-          dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz;
-          dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz;
-          dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz;
-          fl[0] = (-prodnorm2*dprodnorm2[0]*fpair2)*Tap;
-          fl[1] = (-prodnorm2*dprodnorm2[1]*fpair2)*Tap;
-          fl[2] = (-prodnorm2*dprodnorm2[2]*fpair2)*Tap;
-          f[l][0] += fl[0];
-          f[l][1] += fl[1];
-          f[l][2] += fl[2];
-          delli[0] = x[l][0] - x[i][0];
-          delli[1] = x[l][1] - x[i][1];
-          delli[2] = x[l][2] - x[i][2];
-          if (evflag) ev_tally_xyz(l,i,nlocal,newton_pair,0.0,0.0,fl[0],fl[1],fl[2],delli[0],delli[1],delli[2]);
-        }
-
-        if (eflag) {
-          if (tap_flag) evdwl = Tap*Vilp;
-          else  evdwl = Vilp - offset[itype][jtype];
-        }
-
-        if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0,fkcx,fkcy,fkcz,delx,dely,delz);
-      }
-    }
-  }
-  if (vflag_fdotr) virial_fdotr_compute();
-}
-
-/* ----------------------------------------------------------------------
-   Calculate the normals for each atom
-------------------------------------------------------------------------- */
-void PairILPGrapheneHBN::calc_normal()
-{
-  int i,j,ii,jj,inum,jnum;
-  int cont,id,ip,m;
-  double nn,xtp,ytp,ztp,delx,dely,delz,nn2;
-  int *ilist,*jlist;
-  double pv12[3],pv31[3],pv23[3],n1[3],dni[3],dnn[3][3],vet[3][3],dpvdri[3][3];
-  double dn1[3][3][3],dpv12[3][3][3],dpv23[3][3][3],dpv31[3][3][3];
-
-  double **x = atom->x;
-
-  // grow normal array if necessary
-
-  if (atom->nmax > nmax) {
-    memory->destroy(normal);
-    memory->destroy(dnormal);
-    memory->destroy(dnormdri);
-    nmax = atom->nmax;
-    memory->create(normal,nmax,3,"ILPGrapheneHBN:normal");
-    memory->create(dnormdri,3,3,nmax,"ILPGrapheneHBN:dnormdri");
-    memory->create(dnormal,3,3,3,nmax,"ILPGrapheneHBN:dnormal");
-  }
-
-  inum = list->inum;
-  ilist = list->ilist;
-  //Calculate normals
-  for (ii = 0; ii < inum; ii++) {
-    i = ilist[ii];
-    xtp = x[i][0];
-    ytp = x[i][1];
-    ztp = x[i][2];
-
-    //   Initialize the arrays
-    for (id = 0; id < 3; id++){
-      pv12[id] = 0.0;
-      pv31[id] = 0.0;
-      pv23[id] = 0.0;
-      n1[id] = 0.0;
-      dni[id] = 0.0;
-      normal[i][id] = 0.0;
-      for (ip = 0; ip < 3; ip++){
-        vet[ip][id] = 0.0;
-        dnn[ip][id] = 0.0;
-        dpvdri[ip][id] = 0.0;
-        dnormdri[ip][id][i] = 0.0;
-        for (m = 0; m < 3; m++){
-          dpv12[ip][id][m] = 0.0;
-          dpv31[ip][id][m] = 0.0;
-          dpv23[ip][id][m] = 0.0;
-          dn1[ip][id][m] = 0.0;
-          dnormal[ip][id][m][i] = 0.0;
-        }
-      }
-    }
-
-    cont = 0;
-    jlist = ILP_firstneigh[i];
-    jnum = ILP_numneigh[i];
-    for (jj = 0; jj < jnum; jj++) {
-      j = jlist[jj];
-      j &= NEIGHMASK;
-
-      delx = x[j][0] - xtp;
-      dely = x[j][1] - ytp;
-      delz = x[j][2] - ztp;
-      vet[cont][0] = delx;
-      vet[cont][1] = dely;
-      vet[cont][2] = delz;
-      cont++;
-    }
-
-    if (cont <= 1) {
-      normal[i][0] = 0.0;
-      normal[i][1] = 0.0;
-      normal[i][2] = 1.0;
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dnormdri[id][ip][i] = 0.0;
-          for (m = 0; m < 3; m++){
-            dnormal[id][ip][m][i] = 0.0;
-          }
-        }
-      }
-    }
-    else if (cont == 2) {
-      pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2];
-      pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0];
-      pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1];
-      // derivatives of pv12[0] to ri
-      dpvdri[0][0] = 0.0;
-      dpvdri[0][1] = vet[0][2]-vet[1][2];
-      dpvdri[0][2] = vet[1][1]-vet[0][1];
-      // derivatives of pv12[1] to ri
-      dpvdri[1][0] = vet[1][2]-vet[0][2];
-      dpvdri[1][1] = 0.0;
-      dpvdri[1][2] = vet[0][0]-vet[1][0];
-      // derivatives of pv12[2] to ri
-      dpvdri[2][0] = vet[0][1]-vet[1][1];
-      dpvdri[2][1] = vet[1][0]-vet[0][0];
-      dpvdri[2][2] = 0.0;
-
-      dpv12[0][0][0] =  0.0;
-      dpv12[0][1][0] =  vet[1][2];
-      dpv12[0][2][0] = -vet[1][1];
-      dpv12[1][0][0] = -vet[1][2];
-      dpv12[1][1][0] =  0.0;
-      dpv12[1][2][0] =  vet[1][0];
-      dpv12[2][0][0] =  vet[1][1];
-      dpv12[2][1][0] = -vet[1][0];
-      dpv12[2][2][0] =  0.0;
-
-      // derivatives respect to the second neighbor, atom l
-      dpv12[0][0][1] =  0.0;
-      dpv12[0][1][1] = -vet[0][2];
-      dpv12[0][2][1] =  vet[0][1];
-      dpv12[1][0][1] =  vet[0][2];
-      dpv12[1][1][1] =  0.0;
-      dpv12[1][2][1] = -vet[0][0];
-      dpv12[2][0][1] = -vet[0][1];
-      dpv12[2][1][1] =  vet[0][0];
-      dpv12[2][2][1] =  0.0;
-
-      // derivatives respect to the third neighbor, atom n
-      // derivatives of pv12 to rn is zero
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dpv12[id][ip][2] = 0.0;
-        }
-      }
-
-      n1[0] = pv12[0];
-      n1[1] = pv12[1];
-      n1[2] = pv12[2];
-      // the magnitude of the normal vector
-      nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2];
-      nn = sqrt(nn2);
-      if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero");
-      // the unit normal vector
-      normal[i][0] = n1[0]/nn;
-      normal[i][1] = n1[1]/nn;
-      normal[i][2] = n1[2]/nn;
-      // derivatives of nn, dnn:3x1 vector
-      dni[0] = (n1[0]*dpvdri[0][0] + n1[1]*dpvdri[1][0] + n1[2]*dpvdri[2][0])/nn;
-      dni[1] = (n1[0]*dpvdri[0][1] + n1[1]*dpvdri[1][1] + n1[2]*dpvdri[2][1])/nn;
-      dni[2] = (n1[0]*dpvdri[0][2] + n1[1]*dpvdri[1][2] + n1[2]*dpvdri[2][2])/nn;
-      // derivatives of unit vector ni respect to ri, the result is 3x3 matrix
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dnormdri[id][ip][i] = dpvdri[id][ip]/nn - n1[id]*dni[ip]/nn2;
-        }
-      }
-      // derivatives of non-normalized normal vector, dn1:3x3x3 array
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          for (m = 0; m < 3; m++){
-            dn1[id][ip][m] = dpv12[id][ip][m];
-          }
-        }
-      }
-      // derivatives of nn, dnn:3x3 vector
-      // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2
-      // r[id][m]: the id's component of atom m
-      for (m = 0; m < 3; m++){
-        for (id = 0; id < 3; id++){
-          dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn;
-        }
-      }
-      // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2
-      // for atom m, which is a neighbor atom of atom i, m=0,jnum-1
-      for (m = 0; m < 3; m++){
-        for (id = 0; id < 3; id++){
-          for (ip = 0; ip < 3; ip++){
-            dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2;
-          }
-        }
-      }
-    }
-//##############################################################################################
-
-    else if(cont == 3) {
-      pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2];
-      pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0];
-      pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1];
-      // derivatives respect to the first neighbor, atom k
-      dpv12[0][0][0] =  0.0;
-      dpv12[0][1][0] =  vet[1][2];
-      dpv12[0][2][0] = -vet[1][1];
-      dpv12[1][0][0] = -vet[1][2];
-      dpv12[1][1][0] =  0.0;
-      dpv12[1][2][0] =  vet[1][0];
-      dpv12[2][0][0] =  vet[1][1];
-      dpv12[2][1][0] = -vet[1][0];
-      dpv12[2][2][0] =  0.0;
-      // derivatives respect to the second neighbor, atom l
-      dpv12[0][0][1] =  0.0;
-      dpv12[0][1][1] = -vet[0][2];
-      dpv12[0][2][1] =  vet[0][1];
-      dpv12[1][0][1] =  vet[0][2];
-      dpv12[1][1][1] =  0.0;
-      dpv12[1][2][1] = -vet[0][0];
-      dpv12[2][0][1] = -vet[0][1];
-      dpv12[2][1][1] =  vet[0][0];
-      dpv12[2][2][1] =  0.0;
-
-      // derivatives respect to the third neighbor, atom n
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dpv12[id][ip][2] = 0.0;
-        }
-      }
-
-      pv31[0] = vet[2][1]*vet[0][2] - vet[0][1]*vet[2][2];
-      pv31[1] = vet[2][2]*vet[0][0] - vet[0][2]*vet[2][0];
-      pv31[2] = vet[2][0]*vet[0][1] - vet[0][0]*vet[2][1];
-      // derivatives respect to the first neighbor, atom k
-      dpv31[0][0][0] =  0.0;
-      dpv31[0][1][0] = -vet[2][2];
-      dpv31[0][2][0] =  vet[2][1];
-      dpv31[1][0][0] =  vet[2][2];
-      dpv31[1][1][0] =  0.0;
-      dpv31[1][2][0] = -vet[2][0];
-      dpv31[2][0][0] = -vet[2][1];
-      dpv31[2][1][0] =  vet[2][0];
-      dpv31[2][2][0] =  0.0;
-      // derivatives respect to the third neighbor, atom n
-      dpv31[0][0][2] =  0.0;
-      dpv31[0][1][2] =  vet[0][2];
-      dpv31[0][2][2] = -vet[0][1];
-      dpv31[1][0][2] = -vet[0][2];
-      dpv31[1][1][2] =  0.0;
-      dpv31[1][2][2] =  vet[0][0];
-      dpv31[2][0][2] =  vet[0][1];
-      dpv31[2][1][2] = -vet[0][0];
-      dpv31[2][2][2] =  0.0;
-      // derivatives respect to the second neighbor, atom l
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dpv31[id][ip][1] = 0.0;
-        }
-      }
-
-      pv23[0] = vet[1][1]*vet[2][2] - vet[2][1]*vet[1][2];
-      pv23[1] = vet[1][2]*vet[2][0] - vet[2][2]*vet[1][0];
-      pv23[2] = vet[1][0]*vet[2][1] - vet[2][0]*vet[1][1];
-      // derivatives respect to the second neighbor, atom k
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dpv23[id][ip][0] = 0.0;
-        }
-      }
-      // derivatives respect to the second neighbor, atom l
-      dpv23[0][0][1] =  0.0;
-      dpv23[0][1][1] =  vet[2][2];
-      dpv23[0][2][1] = -vet[2][1];
-      dpv23[1][0][1] = -vet[2][2];
-      dpv23[1][1][1] =  0.0;
-      dpv23[1][2][1] =  vet[2][0];
-      dpv23[2][0][1] =  vet[2][1];
-      dpv23[2][1][1] = -vet[2][0];
-      dpv23[2][2][1] =  0.0;
-      // derivatives respect to the third neighbor, atom n
-      dpv23[0][0][2] =  0.0;
-      dpv23[0][1][2] = -vet[1][2];
-      dpv23[0][2][2] =  vet[1][1];
-      dpv23[1][0][2] =  vet[1][2];
-      dpv23[1][1][2] =  0.0;
-      dpv23[1][2][2] = -vet[1][0];
-      dpv23[2][0][2] = -vet[1][1];
-      dpv23[2][1][2] =  vet[1][0];
-      dpv23[2][2][2] =  0.0;
-
-//############################################################################################
-      // average the normal vectors by using the 3 neighboring planes
-      n1[0] = (pv12[0] + pv31[0] + pv23[0])/cont;
-      n1[1] = (pv12[1] + pv31[1] + pv23[1])/cont;
-      n1[2] = (pv12[2] + pv31[2] + pv23[2])/cont;
-      // the magnitude of the normal vector
-      nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2];
-      nn = sqrt(nn2);
-      if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero");
-      // the unit normal vector
-      normal[i][0] = n1[0]/nn;
-      normal[i][1] = n1[1]/nn;
-      normal[i][2] = n1[2]/nn;
-
-      // for the central atoms, dnormdri is always zero
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dnormdri[id][ip][i] = 0.0;
-        }
-      }
-
-      // derivatives of non-normalized normal vector, dn1:3x3x3 array
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          for (m = 0; m < 3; m++){
-            dn1[id][ip][m] = (dpv12[id][ip][m] + dpv23[id][ip][m] + dpv31[id][ip][m])/cont;
-          }
-        }
-      }
-      // derivatives of nn, dnn:3x3 vector
-      // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2
-      // r[id][m]: the id's component of atom m
-      for (m = 0; m < 3; m++){
-        for (id = 0; id < 3; id++){
-          dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn;
-        }
-      }
-      // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2
-      // for atom m, which is a neighbor atom of atom i, m=0,jnum-1
-      for (m = 0; m < 3; m++){
-        for (id = 0; id < 3; id++){
-          for (ip = 0; ip < 3; ip++){
-            dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2;
-          }
-        }
-      }
-    }
-    else {
-      error->one(FLERR,"There are too many neighbors for calculating normals");
-    }
-
-//##############################################################################################
-  }
-}
-
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairILPGrapheneHBN::init_style()
-{
-  if (force->newton_pair == 0)
-    error->all(FLERR,"Pair style ilp/graphene/hbn requires newton pair on");
-  if (!atom->molecule_flag)
-    error->all(FLERR,"Pair style ilp/graphene/hbn requires atom attribute molecule");
-
-  // need a full neighbor list, including neighbors of ghosts
-
-  int irequest = neighbor->request(this,instance_me);
-  neighbor->requests[irequest]->half = 0;
-  neighbor->requests[irequest]->full = 1;
-  neighbor->requests[irequest]->ghost = 1;
-
-  // local ILP neighbor list
-  // create pages if first time or if neighbor pgsize/oneatom has changed
-
-  int create = 0;
-  if (ipage == NULL) create = 1;
-  if (pgsize != neighbor->pgsize) create = 1;
-  if (oneatom != neighbor->oneatom) create = 1;
-
-  if (create) {
-    delete [] ipage;
-    pgsize = neighbor->pgsize;
-    oneatom = neighbor->oneatom;
-
-    int nmypage= comm->nthreads;
-    ipage = new MyPage<int>[nmypage];
-    for (int i = 0; i < nmypage; i++)
-      ipage[i].init(oneatom,pgsize,PGDELTA);
-  }
-}
-
-
-/* ----------------------------------------------------------------------
-   create ILP neighbor list from main neighbor list to calcualte normals
-------------------------------------------------------------------------- */
-
-void PairILPGrapheneHBN::ILP_neigh()
-{
-  int i,j,ii,jj,n,allnum,jnum,itype,jtype;
-  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
-  int *ilist,*jlist,*numneigh,**firstneigh;
-  int *neighptr;
-
-  double **x = atom->x;
-  int *type = atom->type;
-
-  if (atom->nmax > maxlocal) {
-    maxlocal = atom->nmax;
-    memory->destroy(ILP_numneigh);
-    memory->sfree(ILP_firstneigh);
-    memory->create(ILP_numneigh,maxlocal,"ILPGrapheneHBN:numneigh");
-    ILP_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),"ILPGrapheneHBN:firstneigh");
-  }
-
-  allnum = list->inum + list->gnum;
-  ilist = list->ilist;
-  numneigh = list->numneigh;
-  firstneigh = list->firstneigh;
-
-  // store all ILP neighs of owned and ghost atoms
-  // scan full neighbor list of I
-
-  ipage->reset();
-
-  for (ii = 0; ii < allnum; ii++) {
-    i = ilist[ii];
-
-    n = 0;
-    neighptr = ipage->vget();
-
-    xtmp = x[i][0];
-    ytmp = x[i][1];
-    ztmp = x[i][2];
-    itype = map[type[i]];
-    jlist = firstneigh[i];
-    jnum = numneigh[i];
-
-    for (jj = 0; jj < jnum; jj++) {
-      j = jlist[jj];
-      j &= NEIGHMASK;
-      jtype = map[type[j]];
-      delx = xtmp - x[j][0];
-      dely = ytmp - x[j][1];
-      delz = ztmp - x[j][2];
-      rsq = delx*delx + dely*dely + delz*delz;
-
-      if (rsq != 0 && rsq < cutILPsq[itype][jtype] && atom->molecule[i] == atom->molecule[j]) {
-        neighptr[n++] = j;
-      }
-    }
-
-    ILP_firstneigh[i] = neighptr;
-    ILP_numneigh[i] = n;
-    if (n > 3) error->one(FLERR,"There are too many neighbors for some atoms, please check your configuration");
-    ipage->vgot(n);
-    if (ipage->status())
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-  }
-}
-
-
 /* ----------------------------------------------------------------------
    allocate all arrays
 ------------------------------------------------------------------------- */
@@ -1028,6 +386,712 @@ void PairILPGrapheneHBN::read_file(char *filename)
   delete [] words;
 }
 
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairILPGrapheneHBN::init_style()
+{
+  if (force->newton_pair == 0)
+    error->all(FLERR,"Pair style ilp/graphene/hbn requires newton pair on");
+  if (!atom->molecule_flag)
+    error->all(FLERR,"Pair style ilp/graphene/hbn requires atom attribute molecule");
+
+  // need a full neighbor list, including neighbors of ghosts
+
+  int irequest = neighbor->request(this,instance_me);
+  neighbor->requests[irequest]->half = 0;
+  neighbor->requests[irequest]->full = 1;
+  neighbor->requests[irequest]->ghost = 1;
+
+  // local ILP neighbor list
+  // create pages if first time or if neighbor pgsize/oneatom has changed
+
+  int create = 0;
+  if (ipage == NULL) create = 1;
+  if (pgsize != neighbor->pgsize) create = 1;
+  if (oneatom != neighbor->oneatom) create = 1;
+
+  if (create) {
+    delete [] ipage;
+    pgsize = neighbor->pgsize;
+    oneatom = neighbor->oneatom;
+
+    int nmypage= comm->nthreads;
+    ipage = new MyPage<int>[nmypage];
+    for (int i = 0; i < nmypage; i++)
+      ipage[i].init(oneatom,pgsize,PGDELTA);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+void PairILPGrapheneHBN::compute(int eflag, int vflag)
+{
+  ev_init(eflag,vflag);
+  pvector[0] = pvector[1] = 0.0;
+
+  // Build full neighbor list
+  ILP_neigh();
+  // Calculate the normals and its derivatives
+  calc_normal();
+  // Calculate the van der Waals force and energy
+  calc_FvdW(eflag,vflag);
+  // Calculate the repulsive force and energy
+  calc_FRep(eflag,vflag);
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ---------------------------------------------------------------------- 
+   van der Waals forces and energy
+------------------------------------------------------------------------- */
+
+void PairILPGrapheneHBN::calc_FvdW(int eflag, int vflag)
+{
+  int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll;
+  tagint itag,jtag;
+  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
+  double rsq,r,Rcut,r2inv,r6inv,r8inv,Tap,dTap,Vilp,TSvdw,TSvdw2inv,fsum;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+
+  evdwl = 0.0;
+  double **x = atom->x;
+  double **f = atom->f;
+  int *type = atom->type;
+  tagint *tag = atom->tag;
+  int nlocal = atom->nlocal;
+  int newton_pair = force->newton_pair;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // loop over neighbors of my atoms
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    itype = type[i];
+    itag = tag[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+      jtype = type[j];
+      jtag = tag[j];
+
+      // two-body interactions from full neighbor list, skip half of them
+      if (itag > jtag) {
+        if ((itag+jtag) % 2 == 0) continue;
+      } else if (itag < jtag) {
+        if ((itag+jtag) % 2 == 1) continue;
+      } else {
+        if (x[j][2] < ztmp) continue;
+        if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+        if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+      }
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+
+      // only include the interation between different layers
+      if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) {
+
+        int iparam_ij = elem2param[map[itype]][map[jtype]];
+        Param& p = params[iparam_ij];
+
+        r = sqrt(rsq);
+        r2inv = 1.0/rsq;
+        r6inv = r2inv*r2inv*r2inv;
+        r8inv = r6inv*r2inv;
+        // turn on/off taper function
+        if (tap_flag) {
+          Rcut = sqrt(cutsq[itype][jtype]);
+          Tap = calc_Tap(r,Rcut);
+          dTap = calc_dTap(r,Rcut);
+        } else {Tap = 1.0; dTap = 0.0;}
+
+        TSvdw = 1.0 + exp(-p.d*(r/p.seff - 1.0));
+        TSvdw2inv = pow(TSvdw,-2.0);
+        Vilp = -p.C6*r6inv/TSvdw;
+
+        // derivatives
+        fpair = -6.0*p.C6*r8inv/TSvdw + p.C6*p.d/p.seff*(TSvdw-1.0)*TSvdw2inv*r8inv*r;
+	fsum = fpair*Tap - Vilp*dTap/r;
+
+        f[i][0] += fsum*delx;
+        f[i][1] += fsum*dely;
+        f[i][2] += fsum*delz;
+        f[j][0] -= fsum*delx;
+        f[j][1] -= fsum*dely;
+        f[j][2] -= fsum*delz;
+
+        if (eflag) pvector[0] += evdwl = Vilp*Tap;
+        if (evflag) ev_tally(i,j,nlocal,newton_pair,
+                             evdwl,0.0,fsum,delx,dely,delz);
+      }
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- 
+   Repulsive forces and energy
+------------------------------------------------------------------------- */
+
+void PairILPGrapheneHBN::calc_FRep(int eflag, int vflag)
+{
+  int i,j,ii,jj,inum,jnum,itype,jtype,k,kk;
+  double prodnorm1,fkcx,fkcy,fkcz;
+  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1;
+  double rsq,r,Rcut,rhosq1,exp0,exp1,r2inv,r6inv,r8inv,Tap,dTap,Vilp;
+  double frho1,TSvdw,TSvdw2inv,Erep,fsum,rdsq1;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+  int *ILP_neighs_i,*ILP_neighs_j;
+
+  evdwl = 0.0;
+
+  double **x = atom->x;
+  double **f = atom->f;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+  int newton_pair = force->newton_pair;
+  double dprodnorm1[3] = {0.0, 0.0, 0.0};
+  double fp1[3] = {0.0, 0.0, 0.0};
+  double fprod1[3] = {0.0, 0.0, 0.0};
+  double delkj[3] = {0.0, 0.0, 0.0};
+  double fk[3] = {0.0, 0.0, 0.0};
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  //calculate exp(-lambda*(r-z0))*[epsilon/2 + f(rho_ij)]
+  // loop over neighbors of owned atoms
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    if (ILP_numneigh[i] == -1) {
+      continue;
+    }
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    itype = type[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+      if (ILP_numneigh[j] == -1) {
+        continue;
+      }
+      jtype = type[j];
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+
+      // only include the interation between different layers
+      if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) {
+
+        int iparam_ij = elem2param[map[itype]][map[jtype]];
+        Param& p = params[iparam_ij];
+
+        r = sqrt(rsq);
+        // turn on/off taper function
+        if (tap_flag) {
+          Rcut = sqrt(cutsq[itype][jtype]);
+          Tap = calc_Tap(r,Rcut);
+          dTap = calc_dTap(r,Rcut);
+        } else {Tap = 1.0; dTap = 0.0;}
+
+        // Calculate the transverse distance
+        prodnorm1 = normal[i][0]*delx + normal[i][1]*dely + normal[i][2]*delz;
+        rhosq1 = rsq - prodnorm1*prodnorm1;  // rho_ij
+        rdsq1 = rhosq1*p.delta2inv; // (rho_ij/delta)^2
+
+        // store exponents
+        exp0 = exp(-p.lambda*(r-p.z0));
+        exp1 = exp(-rdsq1);
+
+        frho1 = exp1*p.C;
+        Erep = 0.5*p.epsilon + frho1;
+        Vilp = exp0*Erep;
+
+        // derivatives
+        fpair  = p.lambda*exp0/r*Erep;
+        fpair1 = 2.0*exp0*frho1*p.delta2inv;
+        fsum = fpair + fpair1;
+        // derivatives of the product of rij and ni, the result is a vector
+        dprodnorm1[0] = dnormdri[0][0][i]*delx + dnormdri[1][0][i]*dely + dnormdri[2][0][i]*delz;
+        dprodnorm1[1] = dnormdri[0][1][i]*delx + dnormdri[1][1][i]*dely + dnormdri[2][1][i]*delz;
+        dprodnorm1[2] = dnormdri[0][2][i]*delx + dnormdri[1][2][i]*dely + dnormdri[2][2][i]*delz;
+  	fp1[0] = prodnorm1*normal[i][0]*fpair1;
+  	fp1[1] = prodnorm1*normal[i][1]*fpair1;
+  	fp1[2] = prodnorm1*normal[i][2]*fpair1;
+  	fprod1[0] = prodnorm1*dprodnorm1[0]*fpair1;
+  	fprod1[1] = prodnorm1*dprodnorm1[1]*fpair1;
+  	fprod1[2] = prodnorm1*dprodnorm1[2]*fpair1;
+
+        fkcx = (delx*fsum - fp1[0])*Tap - Vilp*dTap*delx/r;
+        fkcy = (dely*fsum - fp1[1])*Tap - Vilp*dTap*dely/r;
+        fkcz = (delz*fsum - fp1[2])*Tap - Vilp*dTap*delz/r;
+
+        f[i][0] += fkcx - fprod1[0]*Tap;
+        f[i][1] += fkcy - fprod1[1]*Tap;
+        f[i][2] += fkcz - fprod1[2]*Tap;
+        f[j][0] -= fkcx;
+        f[j][1] -= fkcy;
+        f[j][2] -= fkcz;
+
+        // calculate the forces acted on the neighbors of atom i from atom j
+        ILP_neighs_i = ILP_firstneigh[i];
+        for (kk = 0; kk < ILP_numneigh[i]; kk++) {
+          k = ILP_neighs_i[kk];
+          if (k == i) continue;
+          // derivatives of the product of rij and ni respect to rk, k=0,1,2, where atom k is the neighbors of atom i
+          dprodnorm1[0] = dnormal[0][0][kk][i]*delx + dnormal[1][0][kk][i]*dely + dnormal[2][0][kk][i]*delz;
+          dprodnorm1[1] = dnormal[0][1][kk][i]*delx + dnormal[1][1][kk][i]*dely + dnormal[2][1][kk][i]*delz;
+          dprodnorm1[2] = dnormal[0][2][kk][i]*delx + dnormal[1][2][kk][i]*dely + dnormal[2][2][kk][i]*delz;
+          fk[0] = (-prodnorm1*dprodnorm1[0]*fpair1)*Tap;
+          fk[1] = (-prodnorm1*dprodnorm1[1]*fpair1)*Tap;
+          fk[2] = (-prodnorm1*dprodnorm1[2]*fpair1)*Tap;
+          f[k][0] += fk[0];
+          f[k][1] += fk[1];
+          f[k][2] += fk[2];
+          delkj[0] = x[k][0] - x[j][0];
+          delkj[1] = x[k][1] - x[j][1];
+          delkj[2] = x[k][2] - x[j][2];
+          if (evflag) ev_tally_xyz(k,j,nlocal,newton_pair,0.0,0.0,fk[0],fk[1],fk[2],delkj[0],delkj[1],delkj[2]);
+        }
+
+        if (eflag) pvector[1] += evdwl = Tap*Vilp;
+        if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0,fkcx,fkcy,fkcz,delx,dely,delz);
+      }
+    } // loop over jj
+  } // loop over ii
+}
+
+/* ----------------------------------------------------------------------
+   create ILP neighbor list from main neighbor list to calcualte normals
+------------------------------------------------------------------------- */
+
+void PairILPGrapheneHBN::ILP_neigh()
+{
+  int i,j,ii,jj,n,allnum,inum,jnum,itype,jtype;
+  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+  int *neighptr;
+
+  double **x = atom->x;
+  int *type = atom->type;
+
+  if (atom->nmax > maxlocal) {
+    maxlocal = atom->nmax;
+    memory->destroy(ILP_numneigh);
+    memory->sfree(ILP_firstneigh);
+    memory->create(ILP_numneigh,maxlocal,"ILPGrapheneHBN:numneigh");
+    ILP_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),"ILPGrapheneHBN:firstneigh");
+  }
+
+  inum = list->inum;
+  allnum = list->inum + list->gnum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // store all ILP neighs of owned and ghost atoms
+  // scan full neighbor list of I
+
+  ipage->reset();
+
+  for (ii = 0; ii < allnum; ii++) {
+    i = ilist[ii];
+
+    n = 0;
+    neighptr = ipage->vget();
+
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    itype = map[type[i]];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+      jtype = map[type[j]];
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+
+      if (rsq != 0 && rsq < cutILPsq[itype][jtype] && atom->molecule[i] == atom->molecule[j]) {
+        neighptr[n++] = j;
+      }
+    } // loop over jj
+
+    ILP_firstneigh[i] = neighptr;
+    if (n == 3) {
+      ILP_numneigh[i] = n;
+    }
+    else if (n < 3) {
+      if (i < inum) {
+        ILP_numneigh[i] = n;
+      } else {
+        ILP_numneigh[i] = -1;
+      }
+    }
+    else if (n > 3) error->one(FLERR,"There are too many neighbors for some atoms, please check your configuration");
+
+    ipage->vgot(n);
+    if (ipage->status())
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+  }
+}
+
+/* ----------------------------------------------------------------------
+   Calculate the normals for each atom
+------------------------------------------------------------------------- */
+void PairILPGrapheneHBN::calc_normal()
+{
+  int i,j,ii,jj,inum,jnum;
+  int cont,id,ip,m;
+  double nn,xtp,ytp,ztp,delx,dely,delz,nn2;
+  int *ilist,*jlist;
+  double pv12[3],pv31[3],pv23[3],n1[3],dni[3],dnn[3][3],vet[3][3],dpvdri[3][3];
+  double dn1[3][3][3],dpv12[3][3][3],dpv23[3][3][3],dpv31[3][3][3];
+
+  double **x = atom->x;
+
+  // grow normal array if necessary
+
+  if (atom->nmax > nmax) {
+    memory->destroy(normal);
+    memory->destroy(dnormal);
+    memory->destroy(dnormdri);
+    nmax = atom->nmax;
+    memory->create(normal,nmax,3,"ILPGrapheneHBN:normal");
+    memory->create(dnormdri,3,3,nmax,"ILPGrapheneHBN:dnormdri");
+    memory->create(dnormal,3,3,3,nmax,"ILPGrapheneHBN:dnormal");
+  }
+
+  inum = list->inum;
+  ilist = list->ilist;
+  //Calculate normals
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+
+    //   Initialize the arrays
+    for (id = 0; id < 3; id++){
+      pv12[id] = 0.0;
+      pv31[id] = 0.0;
+      pv23[id] = 0.0;
+      n1[id] = 0.0;
+      dni[id] = 0.0;
+      normal[i][id] = 0.0;
+      for (ip = 0; ip < 3; ip++){
+        vet[ip][id] = 0.0;
+        dnn[ip][id] = 0.0;
+        dpvdri[ip][id] = 0.0;
+        dnormdri[ip][id][i] = 0.0;
+        for (m = 0; m < 3; m++){
+          dpv12[ip][id][m] = 0.0;
+          dpv31[ip][id][m] = 0.0;
+          dpv23[ip][id][m] = 0.0;
+          dn1[ip][id][m] = 0.0;
+          dnormal[ip][id][m][i] = 0.0;
+        }
+      }
+    }
+
+    if (ILP_numneigh[i] == -1) {
+      continue;
+    }
+    xtp = x[i][0];
+    ytp = x[i][1];
+    ztp = x[i][2];
+
+    cont = 0;
+    jlist = ILP_firstneigh[i];
+    jnum = ILP_numneigh[i];
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+
+      delx = x[j][0] - xtp;
+      dely = x[j][1] - ytp;
+      delz = x[j][2] - ztp;
+      vet[cont][0] = delx;
+      vet[cont][1] = dely;
+      vet[cont][2] = delz;
+      cont++;
+    }
+
+    if (cont <= 1) {
+      normal[i][0] = 0.0;
+      normal[i][1] = 0.0;
+      normal[i][2] = 1.0;
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dnormdri[id][ip][i] = 0.0;
+          for (m = 0; m < 3; m++){
+            dnormal[id][ip][m][i] = 0.0;
+          }
+        }
+      }
+    }
+    else if (cont == 2) {
+      pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2];
+      pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0];
+      pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1];
+      // derivatives of pv12[0] to ri
+      dpvdri[0][0] = 0.0;
+      dpvdri[0][1] = vet[0][2]-vet[1][2];
+      dpvdri[0][2] = vet[1][1]-vet[0][1];
+      // derivatives of pv12[1] to ri
+      dpvdri[1][0] = vet[1][2]-vet[0][2];
+      dpvdri[1][1] = 0.0;
+      dpvdri[1][2] = vet[0][0]-vet[1][0];
+      // derivatives of pv12[2] to ri
+      dpvdri[2][0] = vet[0][1]-vet[1][1];
+      dpvdri[2][1] = vet[1][0]-vet[0][0];
+      dpvdri[2][2] = 0.0;
+
+      dpv12[0][0][0] =  0.0;
+      dpv12[0][1][0] =  vet[1][2];
+      dpv12[0][2][0] = -vet[1][1];
+      dpv12[1][0][0] = -vet[1][2];
+      dpv12[1][1][0] =  0.0;
+      dpv12[1][2][0] =  vet[1][0];
+      dpv12[2][0][0] =  vet[1][1];
+      dpv12[2][1][0] = -vet[1][0];
+      dpv12[2][2][0] =  0.0;
+
+      // derivatives respect to the second neighbor, atom l
+      dpv12[0][0][1] =  0.0;
+      dpv12[0][1][1] = -vet[0][2];
+      dpv12[0][2][1] =  vet[0][1];
+      dpv12[1][0][1] =  vet[0][2];
+      dpv12[1][1][1] =  0.0;
+      dpv12[1][2][1] = -vet[0][0];
+      dpv12[2][0][1] = -vet[0][1];
+      dpv12[2][1][1] =  vet[0][0];
+      dpv12[2][2][1] =  0.0;
+
+      // derivatives respect to the third neighbor, atom n
+      // derivatives of pv12 to rn is zero
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dpv12[id][ip][2] = 0.0;
+        }
+      }
+
+      n1[0] = pv12[0];
+      n1[1] = pv12[1];
+      n1[2] = pv12[2];
+      // the magnitude of the normal vector
+      nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2];
+      nn = sqrt(nn2);
+      if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero");
+      // the unit normal vector
+      normal[i][0] = n1[0]/nn;
+      normal[i][1] = n1[1]/nn;
+      normal[i][2] = n1[2]/nn;
+      // derivatives of nn, dnn:3x1 vector
+      dni[0] = (n1[0]*dpvdri[0][0] + n1[1]*dpvdri[1][0] + n1[2]*dpvdri[2][0])/nn;
+      dni[1] = (n1[0]*dpvdri[0][1] + n1[1]*dpvdri[1][1] + n1[2]*dpvdri[2][1])/nn;
+      dni[2] = (n1[0]*dpvdri[0][2] + n1[1]*dpvdri[1][2] + n1[2]*dpvdri[2][2])/nn;
+      // derivatives of unit vector ni respect to ri, the result is 3x3 matrix
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dnormdri[id][ip][i] = dpvdri[id][ip]/nn - n1[id]*dni[ip]/nn2;
+        }
+      }
+      // derivatives of non-normalized normal vector, dn1:3x3x3 array
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          for (m = 0; m < 3; m++){
+            dn1[id][ip][m] = dpv12[id][ip][m];
+          }
+        }
+      }
+      // derivatives of nn, dnn:3x3 vector
+      // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2
+      // r[id][m]: the id's component of atom m
+      for (m = 0; m < 3; m++){
+        for (id = 0; id < 3; id++){
+          dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn;
+        }
+      }
+      // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2
+      // for atom m, which is a neighbor atom of atom i, m=0,jnum-1
+      for (m = 0; m < 3; m++){
+        for (id = 0; id < 3; id++){
+          for (ip = 0; ip < 3; ip++){
+            dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2;
+          }
+        }
+      }
+    }
+//##############################################################################################
+
+    else if(cont == 3) {
+      pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2];
+      pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0];
+      pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1];
+      // derivatives respect to the first neighbor, atom k
+      dpv12[0][0][0] =  0.0;
+      dpv12[0][1][0] =  vet[1][2];
+      dpv12[0][2][0] = -vet[1][1];
+      dpv12[1][0][0] = -vet[1][2];
+      dpv12[1][1][0] =  0.0;
+      dpv12[1][2][0] =  vet[1][0];
+      dpv12[2][0][0] =  vet[1][1];
+      dpv12[2][1][0] = -vet[1][0];
+      dpv12[2][2][0] =  0.0;
+      // derivatives respect to the second neighbor, atom l
+      dpv12[0][0][1] =  0.0;
+      dpv12[0][1][1] = -vet[0][2];
+      dpv12[0][2][1] =  vet[0][1];
+      dpv12[1][0][1] =  vet[0][2];
+      dpv12[1][1][1] =  0.0;
+      dpv12[1][2][1] = -vet[0][0];
+      dpv12[2][0][1] = -vet[0][1];
+      dpv12[2][1][1] =  vet[0][0];
+      dpv12[2][2][1] =  0.0;
+
+      // derivatives respect to the third neighbor, atom n
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dpv12[id][ip][2] = 0.0;
+        }
+      }
+
+      pv31[0] = vet[2][1]*vet[0][2] - vet[0][1]*vet[2][2];
+      pv31[1] = vet[2][2]*vet[0][0] - vet[0][2]*vet[2][0];
+      pv31[2] = vet[2][0]*vet[0][1] - vet[0][0]*vet[2][1];
+      // derivatives respect to the first neighbor, atom k
+      dpv31[0][0][0] =  0.0;
+      dpv31[0][1][0] = -vet[2][2];
+      dpv31[0][2][0] =  vet[2][1];
+      dpv31[1][0][0] =  vet[2][2];
+      dpv31[1][1][0] =  0.0;
+      dpv31[1][2][0] = -vet[2][0];
+      dpv31[2][0][0] = -vet[2][1];
+      dpv31[2][1][0] =  vet[2][0];
+      dpv31[2][2][0] =  0.0;
+      // derivatives respect to the third neighbor, atom n
+      dpv31[0][0][2] =  0.0;
+      dpv31[0][1][2] =  vet[0][2];
+      dpv31[0][2][2] = -vet[0][1];
+      dpv31[1][0][2] = -vet[0][2];
+      dpv31[1][1][2] =  0.0;
+      dpv31[1][2][2] =  vet[0][0];
+      dpv31[2][0][2] =  vet[0][1];
+      dpv31[2][1][2] = -vet[0][0];
+      dpv31[2][2][2] =  0.0;
+      // derivatives respect to the second neighbor, atom l
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dpv31[id][ip][1] = 0.0;
+        }
+      }
+
+      pv23[0] = vet[1][1]*vet[2][2] - vet[2][1]*vet[1][2];
+      pv23[1] = vet[1][2]*vet[2][0] - vet[2][2]*vet[1][0];
+      pv23[2] = vet[1][0]*vet[2][1] - vet[2][0]*vet[1][1];
+      // derivatives respect to the second neighbor, atom k
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dpv23[id][ip][0] = 0.0;
+        }
+      }
+      // derivatives respect to the second neighbor, atom l
+      dpv23[0][0][1] =  0.0;
+      dpv23[0][1][1] =  vet[2][2];
+      dpv23[0][2][1] = -vet[2][1];
+      dpv23[1][0][1] = -vet[2][2];
+      dpv23[1][1][1] =  0.0;
+      dpv23[1][2][1] =  vet[2][0];
+      dpv23[2][0][1] =  vet[2][1];
+      dpv23[2][1][1] = -vet[2][0];
+      dpv23[2][2][1] =  0.0;
+      // derivatives respect to the third neighbor, atom n
+      dpv23[0][0][2] =  0.0;
+      dpv23[0][1][2] = -vet[1][2];
+      dpv23[0][2][2] =  vet[1][1];
+      dpv23[1][0][2] =  vet[1][2];
+      dpv23[1][1][2] =  0.0;
+      dpv23[1][2][2] = -vet[1][0];
+      dpv23[2][0][2] = -vet[1][1];
+      dpv23[2][1][2] =  vet[1][0];
+      dpv23[2][2][2] =  0.0;
+
+//############################################################################################
+      // average the normal vectors by using the 3 neighboring planes
+      n1[0] = (pv12[0] + pv31[0] + pv23[0])/cont;
+      n1[1] = (pv12[1] + pv31[1] + pv23[1])/cont;
+      n1[2] = (pv12[2] + pv31[2] + pv23[2])/cont;
+      // the magnitude of the normal vector
+      nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2];
+      nn = sqrt(nn2);
+      if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero");
+      // the unit normal vector
+      normal[i][0] = n1[0]/nn;
+      normal[i][1] = n1[1]/nn;
+      normal[i][2] = n1[2]/nn;
+
+      // for the central atoms, dnormdri is always zero
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dnormdri[id][ip][i] = 0.0;
+        }
+      }
+
+      // derivatives of non-normalized normal vector, dn1:3x3x3 array
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          for (m = 0; m < 3; m++){
+            dn1[id][ip][m] = (dpv12[id][ip][m] + dpv23[id][ip][m] + dpv31[id][ip][m])/cont;
+          }
+        }
+      }
+      // derivatives of nn, dnn:3x3 vector
+      // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2
+      // r[id][m]: the id's component of atom m
+      for (m = 0; m < 3; m++){
+        for (id = 0; id < 3; id++){
+          dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn;
+        }
+      }
+      // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2
+      // for atom m, which is a neighbor atom of atom i, m=0,jnum-1
+      for (m = 0; m < 3; m++){
+        for (id = 0; id < 3; id++){
+          for (ip = 0; ip < 3; ip++){
+            dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2;
+          }
+        }
+      }
+    }
+    else {
+      error->one(FLERR,"There are too many neighbors for calculating normals");
+    }
+
+//##############################################################################################
+  }
+}
+
 /* ---------------------------------------------------------------------- */
 
 double PairILPGrapheneHBN::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
@@ -1062,70 +1126,3 @@ double PairILPGrapheneHBN::single(int /*i*/, int /*j*/, int itype, int jtype, do
   philj = Vilp*Tap;
   return factor_lj*philj;
 }
-
-
-/* ---------------------------------------------------------------------- */
-
-int PairILPGrapheneHBN::pack_forward_comm(int n, int *list, double *buf,
-                               int /*pbc_flag*/, int * /*pbc*/)
-{
-  int i,j,m,id,ip,l;
-
-  m = 0;
-  for (i = 0; i < n; i++) {
-    j = list[i];
-    buf[m++] = normal[j][0];
-    buf[m++] = normal[j][1];
-    buf[m++] = normal[j][2];
-    buf[m++] = dnormdri[0][0][j];
-    buf[m++] = dnormdri[0][1][j];
-    buf[m++] = dnormdri[0][2][j];
-    buf[m++] = dnormdri[1][0][j];
-    buf[m++] = dnormdri[1][1][j];
-    buf[m++] = dnormdri[1][2][j];
-    buf[m++] = dnormdri[2][0][j];
-    buf[m++] = dnormdri[2][1][j];
-    buf[m++] = dnormdri[2][2][j];
-    for (l = 0; l < 3; l++){
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          buf[m++] = dnormal[id][ip][l][j];
-        }
-      }
-    }
-  }
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairILPGrapheneHBN::unpack_forward_comm(int n, int first, double *buf)
-{
-  int i,m,last,id,ip,l;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++) {
-    normal[i][0] = buf[m++];
-    normal[i][1] = buf[m++];
-    normal[i][2] = buf[m++];
-    dnormdri[0][0][i] = buf[m++];
-    dnormdri[0][1][i] = buf[m++];
-    dnormdri[0][2][i] = buf[m++];
-    dnormdri[1][0][i] = buf[m++];
-    dnormdri[1][1][i] = buf[m++];
-    dnormdri[1][2][i] = buf[m++];
-    dnormdri[2][0][i] = buf[m++];
-    dnormdri[2][1][i] = buf[m++];
-    dnormdri[2][2][i] = buf[m++];
-    for (l = 0; l < 3; l++){
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dnormal[id][ip][l][i] = buf[m++];
-        }
-      }
-    }
-  }
-}
-
-/* ---------------------------------------------------------------------- */
diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h
index 07c3b2e97b..ec6146fa33 100644
--- a/src/USER-MISC/pair_ilp_graphene_hbn.h
+++ b/src/USER-MISC/pair_ilp_graphene_hbn.h
@@ -21,8 +21,6 @@ PairStyle(ilp/graphene/hbn,PairILPGrapheneHBN)
 #define LMP_PAIR_ILP_GRAPHENE_HBN_H
 
 #include "pair.h"
-#include "my_page.h"
-#include <cmath>
 
 namespace LAMMPS_NS {
 
@@ -36,9 +34,10 @@ class PairILPGrapheneHBN : public Pair {
   void coeff(int, char **);
   double init_one(int, int);
   void init_style();
+  void ILP_neigh();
   void calc_normal();
-  int pack_forward_comm(int, int *, double *, int, int *);
-  void unpack_forward_comm(int, int, double *);
+  void calc_FRep(int, int);
+  void calc_FvdW(int, int);
   double single(int, int, int, int, double, double, double, double &);
 
  protected:
@@ -76,7 +75,6 @@ class PairILPGrapheneHBN : public Pair {
 
   void read_file( char * );
   void allocate();
-  void ILP_neigh();
 
   /* ----Calculate the long-range cutoff term */
   inline double calc_Tap(double r_ij, double Rcut) {
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
index e73278968d..7bfbedfa1c 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
@@ -20,12 +20,11 @@
    [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)]
 ------------------------------------------------------------------------- */
 
+#include "pair_kolmogorov_crespi_full.h"
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 #include <mpi.h>
-#include "pair_kolmogorov_crespi_full.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -49,6 +48,9 @@ PairKolmogorovCrespiFull::PairKolmogorovCrespiFull(LAMMPS *lmp) : Pair(lmp)
   restartinfo = 0;
   one_coeff = 1;
 
+  nextra = 2;
+  pvector = new double[nextra];
+
   // initialize element to parameter maps
   nelements = 0;
   elements = NULL;
@@ -72,8 +74,7 @@ PairKolmogorovCrespiFull::PairKolmogorovCrespiFull(LAMMPS *lmp) : Pair(lmp)
   // always compute energy offset
   offset_flag = 1;
 
-  // set comm size needed by this Pair
-  comm_forward = 39;
+  // turn on the taper function
   tap_flag = 0;
 }
 
@@ -84,6 +85,7 @@ PairKolmogorovCrespiFull::~PairKolmogorovCrespiFull()
   memory->destroy(KC_numneigh);
   memory->sfree(KC_firstneigh);
   delete [] ipage;
+  delete [] pvector;
   memory->destroy(normal);
   memory->destroy(dnormal);
   memory->destroy(dnormdri);
@@ -104,655 +106,6 @@ PairKolmogorovCrespiFull::~PairKolmogorovCrespiFull()
   if (allocated) delete [] map;
 }
 
-/* ---------------------------------------------------------------------- */
-
-void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
-{
-  int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll;
-  tagint itag,jtag;
-  double prodnorm1,prodnorm2,fkcx,fkcy,fkcz;
-  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1,fpair2;
-  double rsq,r,rhosq1,rhosq2,exp0,exp1,exp2,r2inv,r6inv,r8inv,Tap,dTap,Vkc;
-  double frho1,frho2,sumC1,sumC2,sumC11,sumC22,sumCff,fsum,rdsq1,rdsq2;
-  int *ilist,*jlist,*numneigh,**firstneigh;
-  int *KC_neighs_i,*KC_neighs_j;
-
-  evdwl = 0.0;
-  ev_init(eflag,vflag);
-
-  double **x = atom->x;
-  double **f = atom->f;
-  int *type = atom->type;
-  tagint *tag = atom->tag;
-  int nlocal = atom->nlocal;
-  int newton_pair = force->newton_pair;
-  double dprodnorm1[3] = {0.0, 0.0, 0.0};
-  double dprodnorm2[3] = {0.0, 0.0, 0.0};
-  double fp1[3] = {0.0, 0.0, 0.0};
-  double fp2[3] = {0.0, 0.0, 0.0};
-  double fprod1[3] = {0.0, 0.0, 0.0};
-  double fprod2[3] = {0.0, 0.0, 0.0};
-  double fk[3] = {0.0, 0.0, 0.0};
-  double fl[3] = {0.0, 0.0, 0.0};
-  double delkj[3] = {0.0, 0.0, 0.0};
-  double delli[3] = {0.0, 0.0, 0.0};
-
-  inum = list->inum;	
-  ilist = list->ilist;
-  numneigh = list->numneigh;
-  firstneigh = list->firstneigh;
-  // Build full neighbor list
-  KC_neigh();
-  // Calculate the normals
-  calc_normal();
-
-  // communicate the normal vector and its derivatives
-  comm->forward_comm_pair(this);
-
-  // loop over neighbors of my atoms
-  for (ii = 0; ii < inum; ii++) {
-    i = ilist[ii];
-    itag = tag[i];
-    xtmp = x[i][0];
-    ytmp = x[i][1];
-    ztmp = x[i][2];
-    itype = type[i];
-    jlist = firstneigh[i];
-    jnum = numneigh[i];
-
-    for (jj = 0; jj < jnum; jj++) {
-      j = jlist[jj];
-      j &= NEIGHMASK;
-      jtype = type[j];
-      jtag = tag[j];
-
-      // two-body interactions from full neighbor list, skip half of them
-      if (itag > jtag) {
-        if ((itag+jtag) % 2 == 0) continue;
-      } else if (itag < jtag) {
-        if ((itag+jtag) % 2 == 1) continue;
-      } else {
-        if (x[j][2] < ztmp) continue;
-        if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
-        if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
-      }
-
-      delx = xtmp - x[j][0];
-      dely = ytmp - x[j][1];
-      delz = ztmp - x[j][2];
-      rsq = delx*delx + dely*dely + delz*delz;
-
-      // only include the interation between different layers
-      if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) {
-
-        int iparam_ij = elem2param[map[itype]][map[jtype]];
-        Param& p = params[iparam_ij];
-
-        r = sqrt(rsq);
-        r2inv = 1.0/rsq;
-        r6inv = r2inv*r2inv*r2inv;
-        r8inv = r2inv*r6inv;
-	// turn on/off taper function
-	if (tap_flag) {
-	  Tap = calc_Tap(r,sqrt(cutsq[itype][jtype]));
-	  dTap = calc_dTap(r,sqrt(cutsq[itype][jtype]));
-	} else {Tap = 1.0; dTap = 0.0;}
-
-        // Calculate the transverse distance
-        // note that rho_ij does not equal to rho_ji except when normals are all along z
-        prodnorm1 = normal[i][0]*delx + normal[i][1]*dely + normal[i][2]*delz;
-        prodnorm2 = normal[j][0]*delx + normal[j][1]*dely + normal[j][2]*delz;
-        rhosq1 = rsq - prodnorm1*prodnorm1;  // rho_ij
-        rhosq2 = rsq - prodnorm2*prodnorm2;  // rho_ji
-        rdsq1 = rhosq1*p.delta2inv; // (rho_ij/delta)^2
-        rdsq2 = rhosq2*p.delta2inv; // (rho_ji/delta)^2
-
-        // store exponents
-        exp0 = exp(-p.lambda*(r-p.z0));
-        exp1 = exp(-rdsq1);
-        exp2 = exp(-rdsq2);
-
-        sumC1 = p.C0 + p.C2*rdsq1 + p.C4*rdsq1*rdsq1;
-        sumC2 = p.C0 + p.C2*rdsq2 + p.C4*rdsq2*rdsq2;
-        sumC11 = (p.C2 + 2.0*p.C4*rdsq1)*p.delta2inv;
-        sumC22 = (p.C2 + 2.0*p.C4*rdsq2)*p.delta2inv;
-        frho1 = exp1*sumC1;
-        frho2 = exp2*sumC2;
-        sumCff = p.C + frho1 + frho2;
-	Vkc = -p.A*p.z06*r6inv + exp0*sumCff;
-
-        // derivatives
-        fpair = -6.0*p.A*p.z06*r8inv + p.lambda*exp0/r*sumCff;
-        fpair1 = 2.0*exp0*exp1*(p.delta2inv*sumC1 - sumC11);
-        fpair2 = 2.0*exp0*exp2*(p.delta2inv*sumC2 - sumC22);
-        fsum = fpair + fpair1 + fpair2;
-        // derivatives of the product of rij and ni, the result is a vector
-        dprodnorm1[0] = dnormdri[0][0][i]*delx + dnormdri[1][0][i]*dely + dnormdri[2][0][i]*delz;
-        dprodnorm1[1] = dnormdri[0][1][i]*delx + dnormdri[1][1][i]*dely + dnormdri[2][1][i]*delz;
-        dprodnorm1[2] = dnormdri[0][2][i]*delx + dnormdri[1][2][i]*dely + dnormdri[2][2][i]*delz;
-        // derivatives of the product of rji and nj, the result is a vector
-        dprodnorm2[0] = dnormdri[0][0][j]*delx + dnormdri[1][0][j]*dely + dnormdri[2][0][j]*delz;
-        dprodnorm2[1] = dnormdri[0][1][j]*delx + dnormdri[1][1][j]*dely + dnormdri[2][1][j]*delz;
-        dprodnorm2[2] = dnormdri[0][2][j]*delx + dnormdri[1][2][j]*dely + dnormdri[2][2][j]*delz;
-        fp1[0] = prodnorm1*normal[i][0]*fpair1;
-        fp1[1] = prodnorm1*normal[i][1]*fpair1;
-        fp1[2] = prodnorm1*normal[i][2]*fpair1;
-        fp2[0] = prodnorm2*normal[j][0]*fpair2;
-        fp2[1] = prodnorm2*normal[j][1]*fpair2;
-        fp2[2] = prodnorm2*normal[j][2]*fpair2;
-        fprod1[0] = prodnorm1*dprodnorm1[0]*fpair1;
-        fprod1[1] = prodnorm1*dprodnorm1[1]*fpair1;
-        fprod1[2] = prodnorm1*dprodnorm1[2]*fpair1;
-        fprod2[0] = prodnorm2*dprodnorm2[0]*fpair2;
-        fprod2[1] = prodnorm2*dprodnorm2[1]*fpair2;
-        fprod2[2] = prodnorm2*dprodnorm2[2]*fpair2;
-        fkcx = (delx*fsum - fp1[0] - fp2[0])*Tap - Vkc*dTap*delx/r;
-        fkcy = (dely*fsum - fp1[1] - fp2[1])*Tap - Vkc*dTap*dely/r;
-        fkcz = (delz*fsum - fp1[2] - fp2[2])*Tap - Vkc*dTap*delz/r;
-
-        f[i][0] += fkcx - fprod1[0]*Tap;
-        f[i][1] += fkcy - fprod1[1]*Tap;
-        f[i][2] += fkcz - fprod1[2]*Tap;
-        f[j][0] -= fkcx + fprod2[0]*Tap;
-        f[j][1] -= fkcy + fprod2[1]*Tap;
-        f[j][2] -= fkcz + fprod2[2]*Tap;
-
-	// calculate the forces acted on the neighbors of atom i from atom j
-	KC_neighs_i = KC_firstneigh[i];
-	for (kk = 0; kk < KC_numneigh[i]; kk++) {
-	  k = KC_neighs_i[kk];
-          if (k == i) continue;
-          // derivatives of the product of rij and ni respect to rk, k=0,1,2, where atom k is the neighbors of atom i
-          dprodnorm1[0] = dnormal[0][0][kk][i]*delx + dnormal[1][0][kk][i]*dely + dnormal[2][0][kk][i]*delz;
-          dprodnorm1[1] = dnormal[0][1][kk][i]*delx + dnormal[1][1][kk][i]*dely + dnormal[2][1][kk][i]*delz;
-          dprodnorm1[2] = dnormal[0][2][kk][i]*delx + dnormal[1][2][kk][i]*dely + dnormal[2][2][kk][i]*delz;
-          fk[0] = (-prodnorm1*dprodnorm1[0]*fpair1)*Tap;
-          fk[1] = (-prodnorm1*dprodnorm1[1]*fpair1)*Tap;
-          fk[2] = (-prodnorm1*dprodnorm1[2]*fpair1)*Tap;
-          f[k][0] += fk[0];
-          f[k][1] += fk[1];
-          f[k][2] += fk[2];
-          delkj[0] = x[k][0] - x[j][0];
-          delkj[1] = x[k][1] - x[j][1];
-          delkj[2] = x[k][2] - x[j][2];
-          if (evflag) ev_tally_xyz(k,j,nlocal,newton_pair,0.0,0.0,fk[0],fk[1],fk[2],delkj[0],delkj[1],delkj[2]);
-	}
-
-	// calculate the forces acted on the neighbors of atom j from atom i
-	KC_neighs_j = KC_firstneigh[j];
-	for (ll = 0; ll < KC_numneigh[j]; ll++) {
-	  l = KC_neighs_j[ll];
-          if (l == j) continue;
-          // derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j
-          dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz;
-          dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz;
-          dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz;
-          fl[0] = (-prodnorm2*dprodnorm2[0]*fpair2)*Tap;
-          fl[1] = (-prodnorm2*dprodnorm2[1]*fpair2)*Tap;
-          fl[2] = (-prodnorm2*dprodnorm2[2]*fpair2)*Tap;
-          f[l][0] += fl[0];
-          f[l][1] += fl[1];
-          f[l][2] += fl[2];
-          delli[0] = x[l][0] - x[i][0];
-          delli[1] = x[l][1] - x[i][1];
-          delli[2] = x[l][2] - x[i][2];
-          if (evflag) ev_tally_xyz(l,i,nlocal,newton_pair,0.0,0.0,fl[0],fl[1],fl[2],delli[0],delli[1],delli[2]);
-	}
-
-        if (eflag) {
-          if (tap_flag) evdwl = Tap*Vkc;
-          else  evdwl = Vkc - offset[itype][jtype];
-        }
-
-        if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0,fkcx,fkcy,fkcz,delx,dely,delz);
-      }
-    }
-  }
-  if (vflag_fdotr) virial_fdotr_compute();
-}
-
-/* ----------------------------------------------------------------------
-   Calculate the normals for each atom
-------------------------------------------------------------------------- */
-void PairKolmogorovCrespiFull::calc_normal()
-{
-  int i,j,ii,jj,inum,jnum;
-  int cont,id,ip,m;
-  double nn,xtp,ytp,ztp,delx,dely,delz,nn2;
-  int *ilist,*jlist;
-  double pv12[3],pv31[3],pv23[3],n1[3],dni[3],dnn[3][3],vet[3][3],dpvdri[3][3];
-  double dn1[3][3][3],dpv12[3][3][3],dpv23[3][3][3],dpv31[3][3][3];
-
-  double **x = atom->x;
-
-  // grow normal array if necessary
-
-  if (atom->nmax > nmax) {
-    memory->destroy(normal);
-    memory->destroy(dnormal);
-    memory->destroy(dnormdri);
-    nmax = atom->nmax;
-    memory->create(normal,nmax,3,"KolmogorovCrespiFull:normal");
-    memory->create(dnormdri,3,3,nmax,"KolmogorovCrespiFull:dnormdri");
-    memory->create(dnormal,3,3,3,nmax,"KolmogorovCrespiFull:dnormal");
-  }
-
-  inum = list->inum;	
-  ilist = list->ilist;
-  //Calculate normals
-  for (ii = 0; ii < inum; ii++) {
-    i = ilist[ii];
-    xtp = x[i][0];
-    ytp = x[i][1];
-    ztp = x[i][2];
-
-    //   Initialize the arrays
-    for (id = 0; id < 3; id++){
-      pv12[id] = 0.0;
-      pv31[id] = 0.0;
-      pv23[id] = 0.0;
-      n1[id] = 0.0;
-      dni[id] = 0.0;
-      normal[i][id] = 0.0;
-      for (ip = 0; ip < 3; ip++){
-        vet[ip][id] = 0.0;
-        dnn[ip][id] = 0.0;
-        dpvdri[ip][id] = 0.0;
-        dnormdri[ip][id][i] = 0.0;
-        for (m = 0; m < 3; m++){
-          dpv12[ip][id][m] = 0.0;
-          dpv31[ip][id][m] = 0.0;
-          dpv23[ip][id][m] = 0.0;
-          dn1[ip][id][m] = 0.0;
-          dnormal[ip][id][m][i] = 0.0;
-        }
-      }
-    }
-
-    cont = 0;
-    jlist = KC_firstneigh[i];
-    jnum = KC_numneigh[i];
-    for (jj = 0; jj < jnum; jj++) {
-      j = jlist[jj];
-      j &= NEIGHMASK;
-
-      delx = x[j][0] - xtp;
-      dely = x[j][1] - ytp;
-      delz = x[j][2] - ztp;
-      vet[cont][0] = delx;
-      vet[cont][1] = dely;
-      vet[cont][2] = delz;
-      cont++;
-    }
-
-    if (cont <= 1) {
-      normal[i][0] = 0.0;
-      normal[i][1] = 0.0;
-      normal[i][2] = 1.0;
-      // derivatives of normal vector is zero
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dnormdri[id][ip][i] = 0.0;
-          for (m = 0; m < 3; m++){
-            dnormal[id][ip][m][i] = 0.0;
-          }
-        }
-      }
-    }
-    else if (cont == 2) {
-      // for the atoms at the edge who has only two neighbor atoms
-      pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2];
-      pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0];
-      pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1];
-      dpvdri[0][0] = 0.0;
-      dpvdri[0][1] = vet[0][2]-vet[1][2];
-      dpvdri[0][2] = vet[1][1]-vet[0][1];
-      dpvdri[1][0] = vet[1][2]-vet[0][2];
-      dpvdri[1][1] = 0.0;
-      dpvdri[1][2] = vet[0][0]-vet[1][0];
-      dpvdri[2][0] = vet[0][1]-vet[1][1];
-      dpvdri[2][1] = vet[1][0]-vet[0][0];
-      dpvdri[2][2] = 0.0;
-
-      // derivatives respect to the first neighbor, atom k
-      dpv12[0][0][0] =  0.0;
-      dpv12[0][1][0] =  vet[1][2];
-      dpv12[0][2][0] = -vet[1][1];
-      dpv12[1][0][0] = -vet[1][2];
-      dpv12[1][1][0] =  0.0;
-      dpv12[1][2][0] =  vet[1][0];
-      dpv12[2][0][0] =  vet[1][1];
-      dpv12[2][1][0] = -vet[1][0];
-      dpv12[2][2][0] =  0.0;
-
-      // derivatives respect to the second neighbor, atom l
-      dpv12[0][0][1] =  0.0;
-      dpv12[0][1][1] = -vet[0][2];
-      dpv12[0][2][1] =  vet[0][1];
-      dpv12[1][0][1] =  vet[0][2];
-      dpv12[1][1][1] =  0.0;
-      dpv12[1][2][1] = -vet[0][0];
-      dpv12[2][0][1] = -vet[0][1];
-      dpv12[2][1][1] =  vet[0][0];
-      dpv12[2][2][1] =  0.0;
-
-      // derivatives respect to the third neighbor, atom n
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dpv12[id][ip][2] = 0.0;
-        }
-      }
-
-      n1[0] = pv12[0];
-      n1[1] = pv12[1];
-      n1[2] = pv12[2];
-      // the magnitude of the normal vector
-      nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2];
-      nn = sqrt(nn2);
-      if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero");
-      // the unit normal vector
-      normal[i][0] = n1[0]/nn;
-      normal[i][1] = n1[1]/nn;
-      normal[i][2] = n1[2]/nn;
-      // derivatives of nn, dnn:3x1 vector
-      dni[0] = (n1[0]*dpvdri[0][0] + n1[1]*dpvdri[1][0] + n1[2]*dpvdri[2][0])/nn;
-      dni[1] = (n1[0]*dpvdri[0][1] + n1[1]*dpvdri[1][1] + n1[2]*dpvdri[2][1])/nn;
-      dni[2] = (n1[0]*dpvdri[0][2] + n1[1]*dpvdri[1][2] + n1[2]*dpvdri[2][2])/nn;
-      // derivatives of unit vector ni respect to ri, the result is 3x3 matrix
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dnormdri[id][ip][i] = dpvdri[id][ip]/nn - n1[id]*dni[ip]/nn2;
-        }
-      }
-
-      // derivatives of non-normalized normal vector, dn1:3x3x3 array
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          for (m = 0; m < 3; m++){
-            dn1[id][ip][m] = dpv12[id][ip][m];
-          }
-        }
-      }
-      // derivatives of nn, dnn:3x3 vector
-      // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2
-      // r[id][m]: the id's component of atom m
-      for (m = 0; m < 3; m++){
-        for (id = 0; id < 3; id++){
-          dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn;
-        }
-      }
-      // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2
-      // for atom m, which is a neighbor atom of atom i, m=0,jnum-1
-      for (m = 0; m < 3; m++){
-        for (id = 0; id < 3; id++){
-          for (ip = 0; ip < 3; ip++){
-            dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2;
-          }
-        }
-      }
-    }
-//##############################################################################################
-
-    else if(cont == 3) {
-      // for the atoms at the edge who has only two neighbor atoms
-      pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2];
-      pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0];
-      pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1];
-      // derivatives respect to the first neighbor, atom k
-      dpv12[0][0][0] =  0.0;
-      dpv12[0][1][0] =  vet[1][2];
-      dpv12[0][2][0] = -vet[1][1];
-      dpv12[1][0][0] = -vet[1][2];
-      dpv12[1][1][0] =  0.0;
-      dpv12[1][2][0] =  vet[1][0];
-      dpv12[2][0][0] =  vet[1][1];
-      dpv12[2][1][0] = -vet[1][0];
-      dpv12[2][2][0] =  0.0;
-      // derivatives respect to the second neighbor, atom l
-      dpv12[0][0][1] =  0.0;
-      dpv12[0][1][1] = -vet[0][2];
-      dpv12[0][2][1] =  vet[0][1];
-      dpv12[1][0][1] =  vet[0][2];
-      dpv12[1][1][1] =  0.0;
-      dpv12[1][2][1] = -vet[0][0];
-      dpv12[2][0][1] = -vet[0][1];
-      dpv12[2][1][1] =  vet[0][0];
-      dpv12[2][2][1] =  0.0;
-
-      // derivatives respect to the third neighbor, atom n
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dpv12[id][ip][2] = 0.0;
-        }
-      }
-
-      pv31[0] = vet[2][1]*vet[0][2] - vet[0][1]*vet[2][2];
-      pv31[1] = vet[2][2]*vet[0][0] - vet[0][2]*vet[2][0];
-      pv31[2] = vet[2][0]*vet[0][1] - vet[0][0]*vet[2][1];
-      // derivatives respect to the first neighbor, atom k
-      dpv31[0][0][0] =  0.0;
-      dpv31[0][1][0] = -vet[2][2];
-      dpv31[0][2][0] =  vet[2][1];
-      dpv31[1][0][0] =  vet[2][2];
-      dpv31[1][1][0] =  0.0;
-      dpv31[1][2][0] = -vet[2][0];
-      dpv31[2][0][0] = -vet[2][1];
-      dpv31[2][1][0] =  vet[2][0];
-      dpv31[2][2][0] =  0.0;
-      // derivatives respect to the third neighbor, atom n
-      dpv31[0][0][2] =  0.0;
-      dpv31[0][1][2] =  vet[0][2];
-      dpv31[0][2][2] = -vet[0][1];
-      // derivatives of pv13[1] to rn
-      dpv31[1][0][2] = -vet[0][2];
-      dpv31[1][1][2] =  0.0;
-      dpv31[1][2][2] =  vet[0][0];
-      // derivatives of pv13[2] to rn
-      dpv31[2][0][2] =  vet[0][1];
-      dpv31[2][1][2] = -vet[0][0];
-      dpv31[2][2][2] =  0.0;
-
-      // derivatives respect to the second neighbor, atom l
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dpv31[id][ip][1] = 0.0;
-        }
-      }
-
-      pv23[0] = vet[1][1]*vet[2][2] - vet[2][1]*vet[1][2];
-      pv23[1] = vet[1][2]*vet[2][0] - vet[2][2]*vet[1][0];
-      pv23[2] = vet[1][0]*vet[2][1] - vet[2][0]*vet[1][1];
-      // derivatives respect to the second neighbor, atom k
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dpv23[id][ip][0] = 0.0;
-        }
-      }
-      // derivatives respect to the second neighbor, atom l
-      dpv23[0][0][1] =  0.0;
-      dpv23[0][1][1] =  vet[2][2];
-      dpv23[0][2][1] = -vet[2][1];
-      dpv23[1][0][1] = -vet[2][2];
-      dpv23[1][1][1] =  0.0;
-      dpv23[1][2][1] =  vet[2][0];
-      dpv23[2][0][1] =  vet[2][1];
-      dpv23[2][1][1] = -vet[2][0];
-      dpv23[2][2][1] =  0.0;
-      // derivatives respect to the third neighbor, atom n
-      dpv23[0][0][2] =  0.0;
-      dpv23[0][1][2] = -vet[1][2];
-      dpv23[0][2][2] =  vet[1][1];
-      dpv23[1][0][2] =  vet[1][2];
-      dpv23[1][1][2] =  0.0;
-      dpv23[1][2][2] = -vet[1][0];
-      dpv23[2][0][2] = -vet[1][1];
-      dpv23[2][1][2] =  vet[1][0];
-      dpv23[2][2][2] =  0.0;
-
-//############################################################################################
-      // average the normal vectors by using the 3 neighboring planes
-      n1[0] = (pv12[0] + pv31[0] + pv23[0])/cont;
-      n1[1] = (pv12[1] + pv31[1] + pv23[1])/cont;
-      n1[2] = (pv12[2] + pv31[2] + pv23[2])/cont;
-      // the magnitude of the normal vector
-      nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2];
-      nn = sqrt(nn2);
-      if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero");
-      // the unit normal vector
-      normal[i][0] = n1[0]/nn;
-      normal[i][1] = n1[1]/nn;
-      normal[i][2] = n1[2]/nn;
-
-      // for the central atoms, dnormdri is always zero
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          dnormdri[id][ip][i] = 0.0;
-        }
-      } // end of derivatives of normals respect to atom i
-
-      // derivatives of non-normalized normal vector, dn1:3x3x3 array
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-          for (m = 0; m < 3; m++){
-            dn1[id][ip][m] = (dpv12[id][ip][m] + dpv23[id][ip][m] + dpv31[id][ip][m])/cont;
-          }
-        }
-      }
-      // derivatives of nn, dnn:3x3 vector
-      // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2
-      // r[id][m]: the id's component of atom m
-      for (m = 0; m < 3; m++){
-        for (id = 0; id < 3; id++){
-          dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn;
-        }
-      }
-      // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2
-      // for atom m, which is a neighbor atom of atom i, m=0,jnum-1
-      for (m = 0; m < 3; m++){
-        for (id = 0; id < 3; id++){
-          for (ip = 0; ip < 3; ip++){
-            dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2;
-          }
-        }
-      }
-    }
-    else {
-      error->one(FLERR,"There are too many neighbors for calculating normals");
-    }
-
-//##############################################################################################
-  }
-}
-
-/* ----------------------------------------------------------------------
-   init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairKolmogorovCrespiFull::init_style()
-{
-  if (force->newton_pair == 0)
-    error->all(FLERR,"Pair style kolmolgorov/crespi/full requires newton pair on");
-  if (!atom->molecule_flag)
-    error->all(FLERR,"Pair style kolmolgorov/crespi/full requires atom attribute molecule");
-
-  // need a full neighbor list, including neighbors of ghosts
-
-  int irequest = neighbor->request(this,instance_me);
-  neighbor->requests[irequest]->half = 0;
-  neighbor->requests[irequest]->full = 1;
-  neighbor->requests[irequest]->ghost = 1;
-
-  // local KC neighbor list
-  // create pages if first time or if neighbor pgsize/oneatom has changed
-
-  int create = 0;
-  if (ipage == NULL) create = 1;
-  if (pgsize != neighbor->pgsize) create = 1;
-  if (oneatom != neighbor->oneatom) create = 1;
-
-  if (create) {
-    delete [] ipage;
-    pgsize = neighbor->pgsize;
-    oneatom = neighbor->oneatom;
-
-    int nmypage= comm->nthreads;
-    ipage = new MyPage<int>[nmypage];
-    for (int i = 0; i < nmypage; i++)
-      ipage[i].init(oneatom,pgsize,PGDELTA);
-  }
-}
-
-
-/* ----------------------------------------------------------------------
- create neighbor list from main neighbor list for calculating the normals
-------------------------------------------------------------------------- */
-
-void PairKolmogorovCrespiFull::KC_neigh()
-{
-  int i,j,ii,jj,n,allnum,jnum,itype,jtype;
-  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
-  int *ilist,*jlist,*numneigh,**firstneigh;
-  int *neighptr;
-
-  double **x = atom->x;
-  int *type = atom->type;
-
-  if (atom->nmax > maxlocal) {
-    maxlocal = atom->nmax;
-    memory->destroy(KC_numneigh);
-    memory->sfree(KC_firstneigh);
-    memory->create(KC_numneigh,maxlocal,"KolmogorovCrespiFull:numneigh");
-    KC_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),
-                                             "KolmogorovCrespiFull:firstneigh");
-  }
-
-  allnum = list->inum + list->gnum;
-  ilist = list->ilist;
-  numneigh = list->numneigh;
-  firstneigh = list->firstneigh;
-
-  // store all KC neighs of owned and ghost atoms
-  // scan full neighbor list of I
-
-  ipage->reset();
-
-  for (ii = 0; ii < allnum; ii++) {
-    i = ilist[ii];
-
-    n = 0;
-    neighptr = ipage->vget();
-
-    xtmp = x[i][0];
-    ytmp = x[i][1];
-    ztmp = x[i][2];
-    itype = map[type[i]];
-    jlist = firstneigh[i];
-    jnum = numneigh[i];
-
-    for (jj = 0; jj < jnum; jj++) {
-      j = jlist[jj];
-      j &= NEIGHMASK;
-      jtype = map[type[j]];
-      delx = xtmp - x[j][0];
-      dely = ytmp - x[j][1];
-      delz = ztmp - x[j][2];
-      rsq = delx*delx + dely*dely + delz*delz;
-
-      if (rsq != 0 && rsq < cutKCsq[itype][jtype] && atom->molecule[i] == atom->molecule[j]) {
-        neighptr[n++] = j;
-      }
-    }
-
-    KC_firstneigh[i] = neighptr;
-    KC_numneigh[i] = n;
-    if (n > 3) error->one(FLERR,"There are too many neighbors for some atoms, please check your configuration");
-    ipage->vgot(n);
-    if (ipage->status())
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
-  }
-}
-
-
 /* ----------------------------------------------------------------------
    allocate all arrays
 ------------------------------------------------------------------------- */
@@ -1034,6 +387,722 @@ void PairKolmogorovCrespiFull::read_file(char *filename)
   delete [] words;
 }
 
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairKolmogorovCrespiFull::init_style()
+{
+  if (force->newton_pair == 0)
+    error->all(FLERR,"Pair style kolmolgorov/crespi/full requires newton pair on");
+  if (!atom->molecule_flag)
+    error->all(FLERR,"Pair style kolmolgorov/crespi/full requires atom attribute molecule");
+
+  // need a full neighbor list, including neighbors of ghosts
+
+  int irequest = neighbor->request(this,instance_me);
+  neighbor->requests[irequest]->half = 0;
+  neighbor->requests[irequest]->full = 1;
+  neighbor->requests[irequest]->ghost = 1;
+
+  // local KC neighbor list
+  // create pages if first time or if neighbor pgsize/oneatom has changed
+
+  int create = 0;
+  if (ipage == NULL) create = 1;
+  if (pgsize != neighbor->pgsize) create = 1;
+  if (oneatom != neighbor->oneatom) create = 1;
+
+  if (create) {
+    delete [] ipage;
+    pgsize = neighbor->pgsize;
+    oneatom = neighbor->oneatom;
+
+    int nmypage= comm->nthreads;
+    ipage = new MyPage<int>[nmypage];
+    for (int i = 0; i < nmypage; i++)
+      ipage[i].init(oneatom,pgsize,PGDELTA);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
+{
+  ev_init(eflag,vflag);
+  pvector[0] = pvector[1] = 0.0;
+
+  // Build full neighbor list
+  KC_neigh();
+  // Calculate the normals and its derivatives
+  calc_normal();
+  // Calculate the van der Waals force and energy
+  calc_FvdW(eflag,vflag);
+  // Calculate the repulsive force and energy
+  calc_FRep(eflag,vflag);
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ---------------------------------------------------------------------- 
+   van der Waals forces and energy
+------------------------------------------------------------------------- */
+
+void PairKolmogorovCrespiFull::calc_FvdW(int eflag, int vflag)
+{
+  int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll;
+  tagint itag,jtag;
+  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
+  double rsq,r,Rcut,r2inv,r6inv,r8inv,Tap,dTap,Vkc,fsum;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+
+  evdwl = 0.0;
+  double **x = atom->x;
+  double **f = atom->f;
+  int *type = atom->type;
+  tagint *tag = atom->tag;
+  int nlocal = atom->nlocal;
+  int newton_pair = force->newton_pair;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // loop over neighbors of my atoms
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    itype = type[i];
+    itag = tag[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+      jtype = type[j];
+      jtag = tag[j];
+
+      // two-body interactions from full neighbor list, skip half of them
+      if (itag > jtag) {
+        if ((itag+jtag) % 2 == 0) continue;
+      } else if (itag < jtag) {
+        if ((itag+jtag) % 2 == 1) continue;
+      } else {
+        if (x[j][2] < ztmp) continue;
+        if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+        if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+      }
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+
+      // only include the interation between different layers
+      if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) {
+
+        int iparam_ij = elem2param[map[itype]][map[jtype]];
+        Param& p = params[iparam_ij];
+
+        r = sqrt(rsq);
+        r2inv = 1.0/rsq;
+        r6inv = r2inv*r2inv*r2inv;
+        r8inv = r6inv*r2inv;
+        // turn on/off taper function
+        if (tap_flag) {
+          Rcut = sqrt(cutsq[itype][jtype]);
+          Tap = calc_Tap(r,Rcut);
+          dTap = calc_dTap(r,Rcut);
+        } else {Tap = 1.0; dTap = 0.0;}
+
+	Vkc = -p.A*p.z06*r6inv;
+
+        // derivatives
+        fpair = -6.0*p.A*p.z06*r8inv;
+	fsum = fpair*Tap - Vkc*dTap/r;
+
+        f[i][0] += fsum*delx;
+        f[i][1] += fsum*dely;
+        f[i][2] += fsum*delz;
+        f[j][0] -= fsum*delx;
+        f[j][1] -= fsum*dely;
+        f[j][2] -= fsum*delz;
+
+        if (eflag) pvector[0] += evdwl = Vkc*Tap;
+        if (evflag) ev_tally(i,j,nlocal,newton_pair,
+                             evdwl,0.0,fsum,delx,dely,delz);
+      }
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- 
+   Repulsive forces and energy
+------------------------------------------------------------------------- */
+
+void PairKolmogorovCrespiFull::calc_FRep(int eflag, int vflag)
+{
+  int i,j,ii,jj,inum,jnum,itype,jtype,k,kk;
+  double prodnorm1,fkcx,fkcy,fkcz;
+  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1;
+  double rsq,r,rhosq1,exp0,exp1,r2inv,r6inv,r8inv,Tap,dTap,Vkc;
+  double frho_ij,sumC1,sumC11,sumCff,fsum,rho_ij;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+  int *KC_neighs_i,*KC_neighs_j;
+
+  evdwl = 0.0;
+
+  double **x = atom->x;
+  double **f = atom->f;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+  int newton_pair = force->newton_pair;
+  double dprodnorm1[3] = {0.0, 0.0, 0.0};
+  double fp1[3] = {0.0, 0.0, 0.0};
+  double fprod1[3] = {0.0, 0.0, 0.0};
+  double delkj[3] = {0.0, 0.0, 0.0};
+  double fk[3] = {0.0, 0.0, 0.0};
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  //calculate exp(-lambda*(r-z0))*[epsilon/2 + f(rho_ij)]
+  // loop over neighbors of owned atoms
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    if (KC_numneigh[i] == -1) {
+      continue;
+    }
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    itype = type[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+      if (KC_numneigh[j] == -1) {
+        continue;
+      }
+      jtype = type[j];
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+
+      // only include the interation between different layers
+      if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) {
+
+        int iparam_ij = elem2param[map[itype]][map[jtype]];
+        Param& p = params[iparam_ij];
+
+        r = sqrt(rsq);
+        r2inv = 1.0/rsq;
+        r6inv = r2inv*r2inv*r2inv;
+        r8inv = r2inv*r6inv;
+	// turn on/off taper function
+	if (tap_flag) {
+	  Tap = calc_Tap(r,sqrt(cutsq[itype][jtype]));
+	  dTap = calc_dTap(r,sqrt(cutsq[itype][jtype]));
+	} else {Tap = 1.0; dTap = 0.0;}
+
+        // Calculate the transverse distance
+        prodnorm1 = normal[i][0]*delx + normal[i][1]*dely + normal[i][2]*delz;
+        rhosq1 = rsq - prodnorm1*prodnorm1;  // rho_ij
+        rho_ij = rhosq1*p.delta2inv; // (rho_ij/delta)^2
+
+        // store exponents
+        exp0 = exp(-p.lambda*(r-p.z0));
+        exp1 = exp(-rho_ij);
+
+        sumC1 = p.C0 + p.C2*rho_ij + p.C4*rho_ij*rho_ij;
+        sumC11 = (p.C2 + 2.0*p.C4*rho_ij)*p.delta2inv;
+        frho_ij = exp1*sumC1;
+        sumCff = 0.5*p.C + frho_ij;
+	Vkc = exp0*sumCff;
+
+        // derivatives
+        fpair =  p.lambda*exp0/r*sumCff;
+        fpair1 = 2.0*exp0*exp1*(p.delta2inv*sumC1 - sumC11);
+        fsum = fpair + fpair1;
+        // derivatives of the product of rij and ni, the result is a vector
+        dprodnorm1[0] = dnormdri[0][0][i]*delx + dnormdri[1][0][i]*dely + dnormdri[2][0][i]*delz;
+        dprodnorm1[1] = dnormdri[0][1][i]*delx + dnormdri[1][1][i]*dely + dnormdri[2][1][i]*delz;
+        dprodnorm1[2] = dnormdri[0][2][i]*delx + dnormdri[1][2][i]*dely + dnormdri[2][2][i]*delz;
+        fp1[0] = prodnorm1*normal[i][0]*fpair1;
+        fp1[1] = prodnorm1*normal[i][1]*fpair1;
+        fp1[2] = prodnorm1*normal[i][2]*fpair1;
+        fprod1[0] = prodnorm1*dprodnorm1[0]*fpair1;
+        fprod1[1] = prodnorm1*dprodnorm1[1]*fpair1;
+        fprod1[2] = prodnorm1*dprodnorm1[2]*fpair1;
+        fkcx = (delx*fsum - fp1[0])*Tap - Vkc*dTap*delx/r;
+        fkcy = (dely*fsum - fp1[1])*Tap - Vkc*dTap*dely/r;
+        fkcz = (delz*fsum - fp1[2])*Tap - Vkc*dTap*delz/r;
+
+        f[i][0] += fkcx - fprod1[0]*Tap;
+        f[i][1] += fkcy - fprod1[1]*Tap;
+        f[i][2] += fkcz - fprod1[2]*Tap;
+        f[j][0] -= fkcx;
+        f[j][1] -= fkcy;
+        f[j][2] -= fkcz;
+
+	// calculate the forces acted on the neighbors of atom i from atom j
+	KC_neighs_i = KC_firstneigh[i];
+	for (kk = 0; kk < KC_numneigh[i]; kk++) {
+	  k = KC_neighs_i[kk];
+          if (k == i) continue;
+          // derivatives of the product of rij and ni respect to rk, k=0,1,2, where atom k is the neighbors of atom i
+          dprodnorm1[0] = dnormal[0][0][kk][i]*delx + dnormal[1][0][kk][i]*dely + dnormal[2][0][kk][i]*delz;
+          dprodnorm1[1] = dnormal[0][1][kk][i]*delx + dnormal[1][1][kk][i]*dely + dnormal[2][1][kk][i]*delz;
+          dprodnorm1[2] = dnormal[0][2][kk][i]*delx + dnormal[1][2][kk][i]*dely + dnormal[2][2][kk][i]*delz;
+          fk[0] = (-prodnorm1*dprodnorm1[0]*fpair1)*Tap;
+          fk[1] = (-prodnorm1*dprodnorm1[1]*fpair1)*Tap;
+          fk[2] = (-prodnorm1*dprodnorm1[2]*fpair1)*Tap;
+          f[k][0] += fk[0];
+          f[k][1] += fk[1];
+          f[k][2] += fk[2];
+          delkj[0] = x[k][0] - x[j][0];
+          delkj[1] = x[k][1] - x[j][1];
+          delkj[2] = x[k][2] - x[j][2];
+          if (evflag) ev_tally_xyz(k,j,nlocal,newton_pair,0.0,0.0,fk[0],fk[1],fk[2],delkj[0],delkj[1],delkj[2]);
+	}
+
+        if (eflag) {
+          if (tap_flag) pvector[1] += evdwl = Tap*Vkc;
+          else  pvector[1] += evdwl = Vkc - offset[itype][jtype];
+        }
+        if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0,fkcx,fkcy,fkcz,delx,dely,delz);
+      }
+    } // loop over jj
+  } // loop over ii
+}
+
+/* ----------------------------------------------------------------------
+ create neighbor list from main neighbor list for calculating the normals
+------------------------------------------------------------------------- */
+
+void PairKolmogorovCrespiFull::KC_neigh()
+{
+  int i,j,ii,jj,n,allnum,inum,jnum,itype,jtype;
+  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+  int *neighptr;
+
+  double **x = atom->x;
+  int *type = atom->type;
+
+  if (atom->nmax > maxlocal) {
+    maxlocal = atom->nmax;
+    memory->destroy(KC_numneigh);
+    memory->sfree(KC_firstneigh);
+    memory->create(KC_numneigh,maxlocal,"KolmogorovCrespiFull:numneigh");
+    KC_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),
+                                             "KolmogorovCrespiFull:firstneigh");
+  }
+
+  inum = list->inum;
+  allnum = list->inum + list->gnum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // store all KC neighs of owned and ghost atoms
+  // scan full neighbor list of I
+
+  ipage->reset();
+
+  for (ii = 0; ii < allnum; ii++) {
+    i = ilist[ii];
+
+    n = 0;
+    neighptr = ipage->vget();
+
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    itype = map[type[i]];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+      jtype = map[type[j]];
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+
+      if (rsq != 0 && rsq < cutKCsq[itype][jtype] && atom->molecule[i] == atom->molecule[j]) {
+        neighptr[n++] = j;
+      }
+    }
+
+    KC_firstneigh[i] = neighptr;
+    if (n == 3) {
+      KC_numneigh[i] = n;
+    }
+    else if (n < 3) {
+      if (i < inum) {
+        KC_numneigh[i] = n;
+      } else {
+        KC_numneigh[i] = -1;
+      }
+    }
+    else if (n > 3) error->one(FLERR,"There are too many neighbors for some atoms, please check your configuration");
+
+    ipage->vgot(n);
+    if (ipage->status())
+      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+  }
+}
+
+/* ----------------------------------------------------------------------
+   Calculate the normals for each atom
+------------------------------------------------------------------------- */
+void PairKolmogorovCrespiFull::calc_normal()
+{
+  int i,j,ii,jj,inum,jnum;
+  int cont,id,ip,m;
+  double nn,xtp,ytp,ztp,delx,dely,delz,nn2;
+  int *ilist,*jlist;
+  double pv12[3],pv31[3],pv23[3],n1[3],dni[3],dnn[3][3],vet[3][3],dpvdri[3][3];
+  double dn1[3][3][3],dpv12[3][3][3],dpv23[3][3][3],dpv31[3][3][3];
+
+  double **x = atom->x;
+
+  // grow normal array if necessary
+
+  if (atom->nmax > nmax) {
+    memory->destroy(normal);
+    memory->destroy(dnormal);
+    memory->destroy(dnormdri);
+    nmax = atom->nmax;
+    memory->create(normal,nmax,3,"KolmogorovCrespiFull:normal");
+    memory->create(dnormdri,3,3,nmax,"KolmogorovCrespiFull:dnormdri");
+    memory->create(dnormal,3,3,3,nmax,"KolmogorovCrespiFull:dnormal");
+  }
+
+  inum = list->inum;	
+  ilist = list->ilist;
+  //Calculate normals
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+
+    //   Initialize the arrays
+    for (id = 0; id < 3; id++){
+      pv12[id] = 0.0;
+      pv31[id] = 0.0;
+      pv23[id] = 0.0;
+      n1[id] = 0.0;
+      dni[id] = 0.0;
+      normal[i][id] = 0.0;
+      for (ip = 0; ip < 3; ip++){
+        vet[ip][id] = 0.0;
+        dnn[ip][id] = 0.0;
+        dpvdri[ip][id] = 0.0;
+        dnormdri[ip][id][i] = 0.0;
+        for (m = 0; m < 3; m++){
+          dpv12[ip][id][m] = 0.0;
+          dpv31[ip][id][m] = 0.0;
+          dpv23[ip][id][m] = 0.0;
+          dn1[ip][id][m] = 0.0;
+          dnormal[ip][id][m][i] = 0.0;
+        }
+      }
+    }
+
+    if (KC_numneigh[i] == -1) {
+      continue;
+    }
+    xtp = x[i][0];
+    ytp = x[i][1];
+    ztp = x[i][2];
+
+    cont = 0;
+    jlist = KC_firstneigh[i];
+    jnum = KC_numneigh[i];
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+
+      delx = x[j][0] - xtp;
+      dely = x[j][1] - ytp;
+      delz = x[j][2] - ztp;
+      vet[cont][0] = delx;
+      vet[cont][1] = dely;
+      vet[cont][2] = delz;
+      cont++;
+    }
+
+    if (cont <= 1) {
+      normal[i][0] = 0.0;
+      normal[i][1] = 0.0;
+      normal[i][2] = 1.0;
+      // derivatives of normal vector is zero
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dnormdri[id][ip][i] = 0.0;
+          for (m = 0; m < 3; m++){
+            dnormal[id][ip][m][i] = 0.0;
+          }
+        }
+      }
+    }
+    else if (cont == 2) {
+      // for the atoms at the edge who has only two neighbor atoms
+      pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2];
+      pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0];
+      pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1];
+      dpvdri[0][0] = 0.0;
+      dpvdri[0][1] = vet[0][2]-vet[1][2];
+      dpvdri[0][2] = vet[1][1]-vet[0][1];
+      dpvdri[1][0] = vet[1][2]-vet[0][2];
+      dpvdri[1][1] = 0.0;
+      dpvdri[1][2] = vet[0][0]-vet[1][0];
+      dpvdri[2][0] = vet[0][1]-vet[1][1];
+      dpvdri[2][1] = vet[1][0]-vet[0][0];
+      dpvdri[2][2] = 0.0;
+
+      // derivatives respect to the first neighbor, atom k
+      dpv12[0][0][0] =  0.0;
+      dpv12[0][1][0] =  vet[1][2];
+      dpv12[0][2][0] = -vet[1][1];
+      dpv12[1][0][0] = -vet[1][2];
+      dpv12[1][1][0] =  0.0;
+      dpv12[1][2][0] =  vet[1][0];
+      dpv12[2][0][0] =  vet[1][1];
+      dpv12[2][1][0] = -vet[1][0];
+      dpv12[2][2][0] =  0.0;
+
+      // derivatives respect to the second neighbor, atom l
+      dpv12[0][0][1] =  0.0;
+      dpv12[0][1][1] = -vet[0][2];
+      dpv12[0][2][1] =  vet[0][1];
+      dpv12[1][0][1] =  vet[0][2];
+      dpv12[1][1][1] =  0.0;
+      dpv12[1][2][1] = -vet[0][0];
+      dpv12[2][0][1] = -vet[0][1];
+      dpv12[2][1][1] =  vet[0][0];
+      dpv12[2][2][1] =  0.0;
+
+      // derivatives respect to the third neighbor, atom n
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dpv12[id][ip][2] = 0.0;
+        }
+      }
+
+      n1[0] = pv12[0];
+      n1[1] = pv12[1];
+      n1[2] = pv12[2];
+      // the magnitude of the normal vector
+      nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2];
+      nn = sqrt(nn2);
+      if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero");
+      // the unit normal vector
+      normal[i][0] = n1[0]/nn;
+      normal[i][1] = n1[1]/nn;
+      normal[i][2] = n1[2]/nn;
+      // derivatives of nn, dnn:3x1 vector
+      dni[0] = (n1[0]*dpvdri[0][0] + n1[1]*dpvdri[1][0] + n1[2]*dpvdri[2][0])/nn;
+      dni[1] = (n1[0]*dpvdri[0][1] + n1[1]*dpvdri[1][1] + n1[2]*dpvdri[2][1])/nn;
+      dni[2] = (n1[0]*dpvdri[0][2] + n1[1]*dpvdri[1][2] + n1[2]*dpvdri[2][2])/nn;
+      // derivatives of unit vector ni respect to ri, the result is 3x3 matrix
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dnormdri[id][ip][i] = dpvdri[id][ip]/nn - n1[id]*dni[ip]/nn2;
+        }
+      }
+
+      // derivatives of non-normalized normal vector, dn1:3x3x3 array
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          for (m = 0; m < 3; m++){
+            dn1[id][ip][m] = dpv12[id][ip][m];
+          }
+        }
+      }
+      // derivatives of nn, dnn:3x3 vector
+      // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2
+      // r[id][m]: the id's component of atom m
+      for (m = 0; m < 3; m++){
+        for (id = 0; id < 3; id++){
+          dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn;
+        }
+      }
+      // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2
+      // for atom m, which is a neighbor atom of atom i, m=0,jnum-1
+      for (m = 0; m < 3; m++){
+        for (id = 0; id < 3; id++){
+          for (ip = 0; ip < 3; ip++){
+            dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2;
+          }
+        }
+      }
+    }
+//##############################################################################################
+
+    else if(cont == 3) {
+      // for the atoms at the edge who has only two neighbor atoms
+      pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2];
+      pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0];
+      pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1];
+      // derivatives respect to the first neighbor, atom k
+      dpv12[0][0][0] =  0.0;
+      dpv12[0][1][0] =  vet[1][2];
+      dpv12[0][2][0] = -vet[1][1];
+      dpv12[1][0][0] = -vet[1][2];
+      dpv12[1][1][0] =  0.0;
+      dpv12[1][2][0] =  vet[1][0];
+      dpv12[2][0][0] =  vet[1][1];
+      dpv12[2][1][0] = -vet[1][0];
+      dpv12[2][2][0] =  0.0;
+      // derivatives respect to the second neighbor, atom l
+      dpv12[0][0][1] =  0.0;
+      dpv12[0][1][1] = -vet[0][2];
+      dpv12[0][2][1] =  vet[0][1];
+      dpv12[1][0][1] =  vet[0][2];
+      dpv12[1][1][1] =  0.0;
+      dpv12[1][2][1] = -vet[0][0];
+      dpv12[2][0][1] = -vet[0][1];
+      dpv12[2][1][1] =  vet[0][0];
+      dpv12[2][2][1] =  0.0;
+
+      // derivatives respect to the third neighbor, atom n
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dpv12[id][ip][2] = 0.0;
+        }
+      }
+
+      pv31[0] = vet[2][1]*vet[0][2] - vet[0][1]*vet[2][2];
+      pv31[1] = vet[2][2]*vet[0][0] - vet[0][2]*vet[2][0];
+      pv31[2] = vet[2][0]*vet[0][1] - vet[0][0]*vet[2][1];
+      // derivatives respect to the first neighbor, atom k
+      dpv31[0][0][0] =  0.0;
+      dpv31[0][1][0] = -vet[2][2];
+      dpv31[0][2][0] =  vet[2][1];
+      dpv31[1][0][0] =  vet[2][2];
+      dpv31[1][1][0] =  0.0;
+      dpv31[1][2][0] = -vet[2][0];
+      dpv31[2][0][0] = -vet[2][1];
+      dpv31[2][1][0] =  vet[2][0];
+      dpv31[2][2][0] =  0.0;
+      // derivatives respect to the third neighbor, atom n
+      dpv31[0][0][2] =  0.0;
+      dpv31[0][1][2] =  vet[0][2];
+      dpv31[0][2][2] = -vet[0][1];
+      // derivatives of pv13[1] to rn
+      dpv31[1][0][2] = -vet[0][2];
+      dpv31[1][1][2] =  0.0;
+      dpv31[1][2][2] =  vet[0][0];
+      // derivatives of pv13[2] to rn
+      dpv31[2][0][2] =  vet[0][1];
+      dpv31[2][1][2] = -vet[0][0];
+      dpv31[2][2][2] =  0.0;
+
+      // derivatives respect to the second neighbor, atom l
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dpv31[id][ip][1] = 0.0;
+        }
+      }
+
+      pv23[0] = vet[1][1]*vet[2][2] - vet[2][1]*vet[1][2];
+      pv23[1] = vet[1][2]*vet[2][0] - vet[2][2]*vet[1][0];
+      pv23[2] = vet[1][0]*vet[2][1] - vet[2][0]*vet[1][1];
+      // derivatives respect to the second neighbor, atom k
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dpv23[id][ip][0] = 0.0;
+        }
+      }
+      // derivatives respect to the second neighbor, atom l
+      dpv23[0][0][1] =  0.0;
+      dpv23[0][1][1] =  vet[2][2];
+      dpv23[0][2][1] = -vet[2][1];
+      dpv23[1][0][1] = -vet[2][2];
+      dpv23[1][1][1] =  0.0;
+      dpv23[1][2][1] =  vet[2][0];
+      dpv23[2][0][1] =  vet[2][1];
+      dpv23[2][1][1] = -vet[2][0];
+      dpv23[2][2][1] =  0.0;
+      // derivatives respect to the third neighbor, atom n
+      dpv23[0][0][2] =  0.0;
+      dpv23[0][1][2] = -vet[1][2];
+      dpv23[0][2][2] =  vet[1][1];
+      dpv23[1][0][2] =  vet[1][2];
+      dpv23[1][1][2] =  0.0;
+      dpv23[1][2][2] = -vet[1][0];
+      dpv23[2][0][2] = -vet[1][1];
+      dpv23[2][1][2] =  vet[1][0];
+      dpv23[2][2][2] =  0.0;
+
+//############################################################################################
+      // average the normal vectors by using the 3 neighboring planes
+      n1[0] = (pv12[0] + pv31[0] + pv23[0])/cont;
+      n1[1] = (pv12[1] + pv31[1] + pv23[1])/cont;
+      n1[2] = (pv12[2] + pv31[2] + pv23[2])/cont;
+      // the magnitude of the normal vector
+      nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2];
+      nn = sqrt(nn2);
+      if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero");
+      // the unit normal vector
+      normal[i][0] = n1[0]/nn;
+      normal[i][1] = n1[1]/nn;
+      normal[i][2] = n1[2]/nn;
+
+      // for the central atoms, dnormdri is always zero
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          dnormdri[id][ip][i] = 0.0;
+        }
+      } // end of derivatives of normals respect to atom i
+
+      // derivatives of non-normalized normal vector, dn1:3x3x3 array
+      for (id = 0; id < 3; id++){
+        for (ip = 0; ip < 3; ip++){
+          for (m = 0; m < 3; m++){
+            dn1[id][ip][m] = (dpv12[id][ip][m] + dpv23[id][ip][m] + dpv31[id][ip][m])/cont;
+          }
+        }
+      }
+      // derivatives of nn, dnn:3x3 vector
+      // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2
+      // r[id][m]: the id's component of atom m
+      for (m = 0; m < 3; m++){
+        for (id = 0; id < 3; id++){
+          dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn;
+        }
+      }
+      // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2
+      // for atom m, which is a neighbor atom of atom i, m=0,jnum-1
+      for (m = 0; m < 3; m++){
+        for (id = 0; id < 3; id++){
+          for (ip = 0; ip < 3; ip++){
+            dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2;
+          }
+        }
+      }
+    }
+    else {
+      error->one(FLERR,"There are too many neighbors for calculating normals");
+    }
+
+//##############################################################################################
+  }
+}
+
 /* ---------------------------------------------------------------------- */
 
 double PairKolmogorovCrespiFull::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
@@ -1067,69 +1136,3 @@ double PairKolmogorovCrespiFull::single(int /*i*/, int /*j*/, int itype, int jty
   else philj = Vkc - offset[itype][jtype];
   return factor_lj*philj;
 }
-
-/* ---------------------------------------------------------------------- */
-
-int PairKolmogorovCrespiFull::pack_forward_comm(int n, int *list, double *buf,
-                               int /*pbc_flag*/, int * /*pbc*/)
-{
-  int i,j,m,l,ip,id;
-
-  m = 0;
-  for (i = 0; i < n; i++) {
-    j = list[i];
-    buf[m++] = normal[j][0];
-    buf[m++] = normal[j][1];
-    buf[m++] = normal[j][2];
-    buf[m++] = dnormdri[0][0][j];
-    buf[m++] = dnormdri[0][1][j];
-    buf[m++] = dnormdri[0][2][j];
-    buf[m++] = dnormdri[1][0][j];
-    buf[m++] = dnormdri[1][1][j];
-    buf[m++] = dnormdri[1][2][j];
-    buf[m++] = dnormdri[2][0][j];
-    buf[m++] = dnormdri[2][1][j];
-    buf[m++] = dnormdri[2][2][j];
-    for (l = 0; l < 3; l++){
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-	  buf[m++] = dnormal[id][ip][l][j];
-        }
-      }
-    }
-  }
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairKolmogorovCrespiFull::unpack_forward_comm(int n, int first, double *buf)
-{
-  int i,m,last,l,ip,id;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++) {
-    normal[i][0] = buf[m++];
-    normal[i][1] = buf[m++];
-    normal[i][2] = buf[m++];
-    dnormdri[0][0][i] = buf[m++];
-    dnormdri[0][1][i] = buf[m++];
-    dnormdri[0][2][i] = buf[m++];
-    dnormdri[1][0][i] = buf[m++];
-    dnormdri[1][1][i] = buf[m++];
-    dnormdri[1][2][i] = buf[m++];
-    dnormdri[2][0][i] = buf[m++];
-    dnormdri[2][1][i] = buf[m++];
-    dnormdri[2][2][i] = buf[m++];
-    for (l = 0; l < 3; l++){
-      for (id = 0; id < 3; id++){
-        for (ip = 0; ip < 3; ip++){
-	  dnormal[id][ip][l][i] = buf[m++];
-        }
-      }
-    }
-  }
-}
-
-/* ---------------------------------------------------------------------- */
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h
index 9923b409a7..d2971e3fbc 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_full.h
+++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h
@@ -21,8 +21,6 @@ PairStyle(kolmogorov/crespi/full,PairKolmogorovCrespiFull)
 #define LMP_PAIR_KolmogorovCrespi_FULL_H
 
 #include "pair.h"
-#include "my_page.h"
-#include <cmath>
 
 namespace LAMMPS_NS {
 
@@ -36,9 +34,10 @@ class PairKolmogorovCrespiFull : public Pair {
   void coeff(int, char **);
   double init_one(int, int);
   void init_style();
+  void KC_neigh();
   void calc_normal();
-  int pack_forward_comm(int, int *, double *, int, int *);
-  void unpack_forward_comm(int, int, double *);
+  void calc_FRep(int, int);
+  void calc_FvdW(int, int);
   double single(int, int, int, int, double, double, double, double &);
 
  protected:
@@ -77,7 +76,6 @@ class PairKolmogorovCrespiFull : public Pair {
 
   void read_file( char * );
   void allocate();
-  void KC_neigh();
 
 
   /* ----Calculate the long-range cutoff term */
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
index 79d6aa3daf..61c326ac87 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
@@ -21,11 +21,11 @@
    The simplification is that all normals are taken along the z-direction
 ------------------------------------------------------------------------- */
 
+#include "pair_kolmogorov_crespi_z.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_kolmogorov_crespi_z.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_lebedeva_z.cpp b/src/USER-MISC/pair_lebedeva_z.cpp
index c9d90e2850..8930042cef 100644
--- a/src/USER-MISC/pair_lebedeva_z.cpp
+++ b/src/USER-MISC/pair_lebedeva_z.cpp
@@ -22,11 +22,11 @@
    [Lebedeva et al., Physica E, 44(6), 949-954, 2012.]
 ------------------------------------------------------------------------- */
 
+#include "pair_lebedeva_z.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lebedeva_z.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp
index e2e81e4943..50f59107a0 100644
--- a/src/USER-MISC/pair_lennard_mdf.cpp
+++ b/src/USER-MISC/pair_lennard_mdf.cpp
@@ -16,15 +16,13 @@
    Contributing author: Paolo Raiteri (Curtin University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lennard_mdf.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp
index 562a60aa99..2f4e886a61 100644
--- a/src/USER-MISC/pair_list.cpp
+++ b/src/USER-MISC/pair_list.cpp
@@ -16,18 +16,14 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_list.h"
-#include "atom.h"
-#include "comm.h"
-#include "domain.h"
-#include "force.h"
-#include "memory.h"
-
-#include "error.h"
-
-#include <cstdio>
-#include <cstdlib>
+#include <mpi.h>
 #include <cstring>
 #include <cmath>
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "memory.h"
+#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp
index fe21538f2d..ffa828826f 100644
--- a/src/USER-MISC/pair_lj_expand_coul_long.cpp
+++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp
@@ -15,17 +15,15 @@
    Contributing author: Trung Nguyen (Northwestern)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_expand_coul_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp
index cfe125f21f..3fe0fa6bf9 100644
--- a/src/USER-MISC/pair_lj_mdf.cpp
+++ b/src/USER-MISC/pair_lj_mdf.cpp
@@ -16,15 +16,13 @@
    Contributing author: Paolo Raiteri (Curtin University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_mdf.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
index af7d23370d..758962ce29 100644
--- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
+++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
@@ -16,10 +16,10 @@
                          Samuel Genheden (University of Southampton)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_sf_dipole_sf.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp
index f09919ce0f..79e7ac7e09 100644
--- a/src/USER-MISC/pair_meam_spline.cpp
+++ b/src/USER-MISC/pair_meam_spline.cpp
@@ -31,15 +31,13 @@
                        conform with pairing, updated to LAMMPS style
 ------------------------------------------------------------------------- */
 
+#include "pair_meam_spline.h"
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_meam_spline.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
-#include "memory.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp
index af1e8788bd..eeadacf33a 100644
--- a/src/USER-MISC/pair_meam_sw_spline.cpp
+++ b/src/USER-MISC/pair_meam_sw_spline.cpp
@@ -23,15 +23,13 @@
  * 01-Aug-12 - RER: First code version.
 ------------------------------------------------------------------------- */
 
+#include "pair_meam_sw_spline.h"
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_meam_sw_spline.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
-#include "memory.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp
index 1716149a98..29d5715302 100644
--- a/src/USER-MISC/pair_momb.cpp
+++ b/src/USER-MISC/pair_momb.cpp
@@ -16,10 +16,9 @@
                          Ya Zhou (Penn State University)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include "pair_momb.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp
index 7c7973f830..c3cbe39db7 100644
--- a/src/USER-MISC/pair_morse_smooth_linear.cpp
+++ b/src/USER-MISC/pair_morse_smooth_linear.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_morse_smooth_linear.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp
index 01deaf0fbe..416ace8132 100644
--- a/src/USER-MISC/pair_srp.cpp
+++ b/src/USER-MISC/pair_srp.cpp
@@ -25,9 +25,11 @@ There is an example script for this package in examples/USER/srp.
 Please contact Timothy Sirk for questions (tim.sirk@us.army.mil).
 ------------------------------------------------------------------------- */
 
+#include "pair_srp.h"
+#include <mpi.h>
+#include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "pair_srp.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp
index e0985d1dce..5c4f60f354 100644
--- a/src/USER-MISC/pair_tersoff_table.cpp
+++ b/src/USER-MISC/pair_tersoff_table.cpp
@@ -20,11 +20,11 @@
     1) Tersoff, Phys. Rev. B 39, 5566 (1988)
 ------------------------------------------------------------------------- */
 
+#include "pair_tersoff_table.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_tersoff_table.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp
index 031a449689..692f78cf9f 100644
--- a/src/USER-MISC/temper_grem.cpp
+++ b/src/USER-MISC/temper_grem.cpp
@@ -15,26 +15,21 @@
    Contributing author: David Stelter (BU)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "temper_grem.h"
+#include <cmath>
+#include <cstring>
 #include "fix_grem.h"
 #include "universe.h"
 #include "domain.h"
-#include "atom.h"
 #include "update.h"
 #include "integrate.h"
 #include "modify.h"
 #include "compute.h"
 #include "force.h"
-#include "output.h"
-#include "thermo.h"
 #include "fix.h"
 #include "random_park.h"
 #include "finish.h"
 #include "timer.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -76,6 +71,9 @@ void TemperGrem::command(int narg, char **arg)
   nevery = force->inumeric(FLERR,arg[1]);
   double lambda = force->numeric(FLERR,arg[2]);
 
+  // ignore temper command, if walltime limit was already reached
+  if (timer->is_timeout()) return;
+
   // Get and check if gREM fix exists
   for (whichfix = 0; whichfix < modify->nfix; whichfix++)
     if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
@@ -132,6 +130,8 @@ void TemperGrem::command(int narg, char **arg)
   // setup for long tempering run
 
   update->whichflag = 1;
+  timer->init_timeout();
+
   update->nsteps = nsteps;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + nsteps;
@@ -239,7 +239,9 @@ void TemperGrem::command(int narg, char **arg)
 
     // run for nevery timesteps
 
+    timer->init_timeout();
     update->integrate->run(nevery);
+    if (timer->is_timeout()) break;
 
     // compute PE
     // notify compute it will be called at next swap
@@ -247,7 +249,6 @@ void TemperGrem::command(int narg, char **arg)
     pe = pe_compute->compute_scalar();
     pe_compute->addstep(update->ntimestep + nevery);
 
-
     // which = which of 2 kinds of swaps to do (0,1)
 
     if (!ranswap) which = iswap % 2;
diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp
index 7cf8fbab9b..55c9aadc6f 100644
--- a/src/USER-MISC/temper_npt.cpp
+++ b/src/USER-MISC/temper_npt.cpp
@@ -17,10 +17,9 @@
    Contact Email: amulyapervaje@gmail.com
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "temper_npt.h"
+#include <cmath>
+#include <cstring>
 #include "universe.h"
 #include "domain.h"
 #include "atom.h"
@@ -29,14 +28,12 @@
 #include "modify.h"
 #include "compute.h"
 #include "force.h"
-#include "output.h"
-#include "thermo.h"
 #include "fix.h"
 #include "random_park.h"
 #include "finish.h"
 #include "timer.h"
-#include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -77,6 +74,10 @@ void TemperNPT::command(int narg, char **arg)
   double temp = force->numeric(FLERR,arg[2]);
   double press_set = force->numeric(FLERR,arg[6]);
 
+  // ignore temper command, if walltime limit was already reached
+
+  if (timer->is_timeout()) return;
+
   for (whichfix = 0; whichfix < modify->nfix; whichfix++)
     if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
   if (whichfix == modify->nfix)
@@ -101,13 +102,15 @@ void TemperNPT::command(int narg, char **arg)
   // change the volume. This currently only applies to fix npt and
   // fix rigid/npt variants
 
-  if ((strncmp(modify->fix[whichfix]->style,"npt",3) != 0)
-      && (strncmp(modify->fix[whichfix]->style,"rigid/npt",9) != 0))
+  if ( (!utils::strmatch(modify->fix[whichfix]->style,"^npt")) &&
+       (!utils::strmatch(modify->fix[whichfix]->style,"^rigid/npt")) )
     error->universe_all(FLERR,"Tempering temperature and pressure fix is not supported");
 
   // setup for long tempering run
 
   update->whichflag = 1;
+  timer->init_timeout();
+
   update->nsteps = nsteps;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + nsteps;
@@ -215,7 +218,9 @@ void TemperNPT::command(int narg, char **arg)
 
     // run for nevery timesteps
 
+    timer->init_timeout();
     update->integrate->run(nevery);
+    if (timer->is_timeout()) break;
 
     // compute PE
     // notify compute it will be called at next swap
diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp
index e8e6f279de..bb0a01d546 100644
--- a/src/USER-MOFFF/angle_class2_p6.cpp
+++ b/src/USER-MOFFF/angle_class2_p6.cpp
@@ -16,10 +16,10 @@
                         and Rochus Schmid (Ruhr-Universitaet Bochum)
 ------------------------------------------------------------------------- */
 
+#include "angle_class2_p6.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "angle_class2_p6.h"
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/USER-MOFFF/angle_class2_p6.h b/src/USER-MOFFF/angle_class2_p6.h
index b583a45b19..f2f324c0c6 100644
--- a/src/USER-MOFFF/angle_class2_p6.h
+++ b/src/USER-MOFFF/angle_class2_p6.h
@@ -20,7 +20,6 @@ AngleStyle(class2/p6,AngleClass2P6)
 #ifndef LMP_ANGLE_CLASS2_P6_H
 #define LMP_ANGLE_CLASS2_P6_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp
index 3829d2b8dc..c17b2a1dba 100644
--- a/src/USER-MOFFF/angle_cosine_buck6d.cpp
+++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp
@@ -16,9 +16,9 @@
                         and Rochus Schmid (Ruhr-Universitaet Bochum)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "angle_cosine_buck6d.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
@@ -26,13 +26,11 @@
 #include "force.h"
 #include "pair.h"
 #include "math_const.h"
-#include "math_special.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
-using namespace MathSpecial;
 
 #define SMALL 0.001
 
diff --git a/src/USER-MOFFF/angle_cosine_buck6d.h b/src/USER-MOFFF/angle_cosine_buck6d.h
index 689b1634e0..1d0df10228 100644
--- a/src/USER-MOFFF/angle_cosine_buck6d.h
+++ b/src/USER-MOFFF/angle_cosine_buck6d.h
@@ -20,7 +20,6 @@ AngleStyle(cosine/buck6d, AngleCosineBuck6d)
 #ifndef LMP_ANGLE_COSINE_BUCK6D_H
 #define LMP_ANGLE_COSINE_BUCK6D_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp
index 3f1e61e54a..12f7062ccc 100644
--- a/src/USER-MOFFF/improper_inversion_harmonic.cpp
+++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp
@@ -19,17 +19,13 @@
    [ abbreviated from and verified via DLPOLY2.0 ]
 ------------------------------------------------------------------------- */
 
+#include "improper_inversion_harmonic.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
-#include <cstring>
-#include "improper_inversion_harmonic.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
-#include "update.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-MOFFF/improper_inversion_harmonic.h b/src/USER-MOFFF/improper_inversion_harmonic.h
index 201c9e358d..206b40aebf 100644
--- a/src/USER-MOFFF/improper_inversion_harmonic.h
+++ b/src/USER-MOFFF/improper_inversion_harmonic.h
@@ -20,7 +20,6 @@ ImproperStyle(inversion/harmonic,ImproperInversionHarmonic)
 #ifndef LMP_IMPROPER_INVERSION_HARMONIC_H
 #define LMP_IMPROPER_INVERSION_HARMONIC_H
 
-#include <cstdio>
 #include "improper.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
index 282bb0c58f..9c917d1c19 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
@@ -18,11 +18,9 @@
                Fennell and Gezelter, JCP 124, 234104 (2006)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_buck6d_coul_gauss_dsf.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
index d6a4121d21..953507ce21 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
@@ -17,11 +17,10 @@
    References: Bureekaew and Schmid, Phys. Status Solidi B 250, 1128 (2013)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_buck6d_coul_gauss_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -29,12 +28,10 @@
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "memory.h"
-#include "math_const.h"
 #include "error.h"
 #include "math_special.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define EWALD_F   1.12837917
 
diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/USER-MOLFILE/dump_molfile.cpp
index 732fea74bd..d9d8ec3c97 100644
--- a/src/USER-MOLFILE/dump_molfile.cpp
+++ b/src/USER-MOLFILE/dump_molfile.cpp
@@ -15,15 +15,14 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
+#include "dump_molfile.h"
+#include <mpi.h>
 #include <cstring>
 #include <cmath>
-#include "dump_molfile.h"
 #include "domain.h"
 #include "atom.h"
 #include "comm.h"
 #include "update.h"
-#include "output.h"
 #include "group.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp
index ca1a61850c..5cff56753b 100644
--- a/src/USER-MOLFILE/reader_molfile.cpp
+++ b/src/USER-MOLFILE/reader_molfile.cpp
@@ -15,11 +15,9 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
+#include "reader_molfile.h"
 #include <cstdlib>
 #include <cmath>
-#include "reader_molfile.h"
-#include "atom.h"
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp
index 118ba00226..f135446915 100644
--- a/src/USER-OMP/angle_charmm_omp.cpp
+++ b/src/USER-OMP/angle_charmm_omp.cpp
@@ -16,19 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_charmm_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define SMALL 0.001
 
diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp
index e072d136e1..0cf5489663 100644
--- a/src/USER-OMP/angle_class2_omp.cpp
+++ b/src/USER-OMP/angle_class2_omp.cpp
@@ -16,19 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_class2_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define SMALL 0.001
 
diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp
index a6dfb20433..7f4d994c4f 100644
--- a/src/USER-OMP/angle_cosine_delta_omp.cpp
+++ b/src/USER-OMP/angle_cosine_delta_omp.cpp
@@ -16,19 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_cosine_delta_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define SMALL 0.001
 
diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp
index 9097c8569c..0543c94799 100644
--- a/src/USER-OMP/angle_cosine_omp.cpp
+++ b/src/USER-OMP/angle_cosine_omp.cpp
@@ -16,19 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_cosine_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define SMALL 0.001
 
diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp
index 3fcea7ad1d..907315f83b 100644
--- a/src/USER-OMP/angle_cosine_periodic_omp.cpp
+++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp
@@ -16,20 +16,16 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_cosine_periodic_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
+#include "timer.h"
 #include "math_special.h"
 
-#include <cmath>
-
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace MathSpecial;
 
 #define SMALL 0.001
diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp
index 6bd2feb023..6c42319905 100644
--- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp
+++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp
@@ -16,19 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_cosine_shift_exp_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define SMALL 0.001
 
diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp
index 56486faac1..5c0afcf316 100644
--- a/src/USER-OMP/angle_cosine_shift_omp.cpp
+++ b/src/USER-OMP/angle_cosine_shift_omp.cpp
@@ -16,19 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_cosine_shift_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define SMALL 0.001
 
diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp
index 6dd2a3bb3b..27c47b90d8 100644
--- a/src/USER-OMP/angle_cosine_squared_omp.cpp
+++ b/src/USER-OMP/angle_cosine_squared_omp.cpp
@@ -16,19 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_cosine_squared_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define SMALL 0.001
 
diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp
index da2e819ee2..6af5b44a03 100644
--- a/src/USER-OMP/angle_dipole_omp.cpp
+++ b/src/USER-OMP/angle_dipole_omp.cpp
@@ -16,20 +16,16 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_dipole_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define SMALL 0.001
 
diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/USER-OMP/angle_fourier_omp.cpp
index b2f9b47e05..98527c2028 100644
--- a/src/USER-OMP/angle_fourier_omp.cpp
+++ b/src/USER-OMP/angle_fourier_omp.cpp
@@ -16,19 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_fourier_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define SMALL 0.001
 
diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/USER-OMP/angle_fourier_simple_omp.cpp
index 93532a30e5..71d0197b72 100644
--- a/src/USER-OMP/angle_fourier_simple_omp.cpp
+++ b/src/USER-OMP/angle_fourier_simple_omp.cpp
@@ -16,19 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_fourier_simple_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define SMALL 0.001
 
diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp
index 824b254287..ee08bbd8ad 100644
--- a/src/USER-OMP/angle_harmonic_omp.cpp
+++ b/src/USER-OMP/angle_harmonic_omp.cpp
@@ -16,19 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_harmonic_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define SMALL 0.001
 
diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/USER-OMP/angle_quartic_omp.cpp
index fff08ddb39..5745948222 100644
--- a/src/USER-OMP/angle_quartic_omp.cpp
+++ b/src/USER-OMP/angle_quartic_omp.cpp
@@ -16,19 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_quartic_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define SMALL 0.001
 
diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp
index e8c762092c..e0b1da0baf 100644
--- a/src/USER-OMP/angle_sdk_omp.cpp
+++ b/src/USER-OMP/angle_sdk_omp.cpp
@@ -16,20 +16,16 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_sdk_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "comm.h"
 #include "force.h"
-#include "math_const.h"
-
-#include <cmath>
-
 #include "lj_sdk_common.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace LJSDKParms;
 
 #define SMALL 0.001
diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp
index d9d80b744d..4f6edf2073 100644
--- a/src/USER-OMP/angle_table_omp.cpp
+++ b/src/USER-OMP/angle_table_omp.cpp
@@ -16,19 +16,15 @@
 ------------------------------------------------------------------------- */
 
 #include "angle_table_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include "math_const.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define SMALL 0.001
 
diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp
index fdd73c20b0..7d1b693faf 100644
--- a/src/USER-OMP/bond_class2_omp.cpp
+++ b/src/USER-OMP/bond_class2_omp.cpp
@@ -20,7 +20,7 @@
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 
 #include <cmath>
 
diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp
index a8eec11760..aefae6dcf7 100644
--- a/src/USER-OMP/bond_fene_expand_omp.cpp
+++ b/src/USER-OMP/bond_fene_expand_omp.cpp
@@ -20,7 +20,7 @@
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "error.h"
 #include "update.h"
 
diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp
index be7dcd4b49..2b579114ba 100644
--- a/src/USER-OMP/bond_fene_omp.cpp
+++ b/src/USER-OMP/bond_fene_omp.cpp
@@ -20,7 +20,7 @@
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "error.h"
 #include "update.h"
 
diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/USER-OMP/bond_gromos_omp.cpp
index 8f0926c0e9..ba23217a1f 100644
--- a/src/USER-OMP/bond_gromos_omp.cpp
+++ b/src/USER-OMP/bond_gromos_omp.cpp
@@ -20,9 +20,7 @@
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
-
-#include <cmath>
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/USER-OMP/bond_harmonic_omp.cpp
index a3bb69c53c..5515284f9a 100644
--- a/src/USER-OMP/bond_harmonic_omp.cpp
+++ b/src/USER-OMP/bond_harmonic_omp.cpp
@@ -20,7 +20,7 @@
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 
 #include <cmath>
 
diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
index 5c16e27a32..a871fa8c04 100644
--- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
+++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
@@ -20,7 +20,7 @@
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 
 #include <cmath>
 
diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp
index 39e957c137..4117da9159 100644
--- a/src/USER-OMP/bond_harmonic_shift_omp.cpp
+++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp
@@ -20,7 +20,7 @@
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 
 #include <cmath>
 
diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp
index c0203de0d6..e6526dc8dc 100644
--- a/src/USER-OMP/bond_morse_omp.cpp
+++ b/src/USER-OMP/bond_morse_omp.cpp
@@ -20,7 +20,7 @@
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 
 #include <cmath>
 
diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp
index 8fa3daf8ab..0d1a648415 100644
--- a/src/USER-OMP/bond_nonlinear_omp.cpp
+++ b/src/USER-OMP/bond_nonlinear_omp.cpp
@@ -20,7 +20,7 @@
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 
 #include <cmath>
 
diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp
index fd0ccaf79d..60d3a5601c 100644
--- a/src/USER-OMP/bond_quartic_omp.cpp
+++ b/src/USER-OMP/bond_quartic_omp.cpp
@@ -20,7 +20,7 @@
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "pair.h"
 
 #include <cmath>
diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp
index 1616988385..8e1e792c73 100644
--- a/src/USER-OMP/bond_table_omp.cpp
+++ b/src/USER-OMP/bond_table_omp.cpp
@@ -20,7 +20,7 @@
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 
 #include <cmath>
 
diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp
index b09863613e..95ad9af6a6 100644
--- a/src/USER-OMP/dihedral_charmm_omp.cpp
+++ b/src/USER-OMP/dihedral_charmm_omp.cpp
@@ -15,13 +15,12 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cmath>
 #include "dihedral_charmm_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "pair.h"
 #include "update.h"
diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp
index 03ac9d9bab..6c2bc02ff4 100644
--- a/src/USER-OMP/dihedral_class2_omp.cpp
+++ b/src/USER-OMP/dihedral_class2_omp.cpp
@@ -20,7 +20,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
index c64cad9fc3..d77e9d6b3e 100644
--- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
+++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
@@ -20,7 +20,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp
index 94bdae3795..93dbd773ca 100644
--- a/src/USER-OMP/dihedral_fourier_omp.cpp
+++ b/src/USER-OMP/dihedral_fourier_omp.cpp
@@ -15,20 +15,18 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "dihedral_fourier_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
 
-#include "math_const.h"
 #include "suffix.h"
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define TOLERANCE 0.05
 
diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp
index 10ccbd3d9f..84aa584d9e 100644
--- a/src/USER-OMP/dihedral_harmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_harmonic_omp.cpp
@@ -20,7 +20,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp
index 8c8e29cac0..51b07754e2 100644
--- a/src/USER-OMP/dihedral_helix_omp.cpp
+++ b/src/USER-OMP/dihedral_helix_omp.cpp
@@ -20,7 +20,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "update.h"
 #include "math_const.h"
diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
index 38961e1746..4cb6919a96 100644
--- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
@@ -20,7 +20,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp
index e74238265d..203884531b 100644
--- a/src/USER-OMP/dihedral_nharmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp
@@ -20,10 +20,10 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp
index 64eaffe6fe..af12bb866e 100644
--- a/src/USER-OMP/dihedral_opls_omp.cpp
+++ b/src/USER-OMP/dihedral_opls_omp.cpp
@@ -20,7 +20,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp
index 8df622b847..8cea62aaea 100644
--- a/src/USER-OMP/dihedral_quadratic_omp.cpp
+++ b/src/USER-OMP/dihedral_quadratic_omp.cpp
@@ -20,10 +20,10 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/dihedral_table_omp.cpp b/src/USER-OMP/dihedral_table_omp.cpp
index 792ee90c26..6b10027b9d 100644
--- a/src/USER-OMP/dihedral_table_omp.cpp
+++ b/src/USER-OMP/dihedral_table_omp.cpp
@@ -15,19 +15,14 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstdio>
-
 #include "dihedral_table_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
 #include "domain.h"
+#include "neighbor.h"
 #include "force.h"
-#include "update.h"
-#include "error.h"
-
+#include "timer.h"
 #include "math_const.h"
 #include "math_extra.h"
 
diff --git a/src/USER-OMP/domain_omp.cpp b/src/USER-OMP/domain_omp.cpp
index 584e56b1f0..a18931c551 100644
--- a/src/USER-OMP/domain_omp.cpp
+++ b/src/USER-OMP/domain_omp.cpp
@@ -15,7 +15,6 @@
    Contributing author : Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include "domain.h"
 #include "accelerator_omp.h"
 #include "atom.h"
 
diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp
index b56fc25142..aadf63741d 100644
--- a/src/USER-OMP/ewald_omp.cpp
+++ b/src/USER-OMP/ewald_omp.cpp
@@ -15,15 +15,14 @@
    Contributing authors: Roy Pollock (LLNL), Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "ewald_omp.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
-
-#include <cmath>
-
+#include "timer.h"
 #include "math_const.h"
 
 #include "suffix.h"
diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/USER-OMP/fix_gravity_omp.cpp
index eae918ec52..fa6b698821 100644
--- a/src/USER-OMP/fix_gravity_omp.cpp
+++ b/src/USER-OMP/fix_gravity_omp.cpp
@@ -15,19 +15,12 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "fix_gravity_omp.h"
 #include "atom.h"
 #include "update.h"
-#include "domain.h"
 #include "input.h"
 #include "modify.h"
-#include "respa.h"
 #include "variable.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/USER-OMP/fix_neigh_history_omp.cpp
index efa7f5a3f1..22d3fa944c 100644
--- a/src/USER-OMP/fix_neigh_history_omp.cpp
+++ b/src/USER-OMP/fix_neigh_history_omp.cpp
@@ -11,18 +11,14 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdio>
 #include "fix_neigh_history_omp.h"
+#include <cstring>
+#include "my_page.h"
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "force.h"
 #include "pair.h"
-#include "update.h"
 #include "memory.h"
-#include "modify.h"
 #include "error.h"
 
 #if defined(_OPENMP)
@@ -175,6 +171,8 @@ void FixNeighHistoryOMP::pre_exchange_onesided()
     }
 
     // set maxpartner = max # of partners of any owned atom
+    // maxexchange = max # of values for any Comm::exchange() atom
+
     maxpartner = m = 0;
     for (i = lfrom; i < lto; i++)
       m = MAX(m,npartner[i]);
@@ -184,7 +182,7 @@ void FixNeighHistoryOMP::pre_exchange_onesided()
 #endif
     {
       maxpartner = MAX(m,maxpartner);
-      comm->maxexchange_fix =MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
+      maxexchange = (dnum+1)*maxpartner+1;
     }
   }
 
@@ -347,6 +345,7 @@ void FixNeighHistoryOMP::pre_exchange_newton()
     }
 
     // set maxpartner = max # of partners of any owned atom
+    // maxexchange = max # of values for any Comm::exchange() atom
     m = 0;
     for (i = lfrom; i < lto; i++)
       m = MAX(m,npartner[i]);
@@ -356,7 +355,7 @@ void FixNeighHistoryOMP::pre_exchange_newton()
 #endif
     {
       maxpartner = MAX(m,maxpartner);
-      comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
+      maxexchange = (dnum+1)*maxpartner+1;
     }
   }
 
@@ -485,6 +484,8 @@ void FixNeighHistoryOMP::pre_exchange_no_newton()
     }
 
     // set maxpartner = max # of partners of any owned atom
+    // maxexchange = max # of values for any Comm::exchange() atom
+
     m = 0;
     for (i = lfrom; i < lto; i++)
       m = MAX(m,npartner[i]);
@@ -494,7 +495,7 @@ void FixNeighHistoryOMP::pre_exchange_no_newton()
 #endif
     {
       maxpartner = MAX(m,maxpartner);
-      comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
+      maxexchange = (dnum+1)*maxpartner+1;
     }
   }
 }
diff --git a/src/USER-OMP/fix_nh_omp.cpp b/src/USER-OMP/fix_nh_omp.cpp
index 76a47b71fd..2abd739f71 100644
--- a/src/USER-OMP/fix_nh_omp.cpp
+++ b/src/USER-OMP/fix_nh_omp.cpp
@@ -16,15 +16,13 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_nh_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "compute.h"
 #include "domain.h"
 #include "error.h"
 #include "modify.h"
 
-#include <cmath>
-#include <cstdio>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
diff --git a/src/USER-OMP/fix_nh_sphere_omp.cpp b/src/USER-OMP/fix_nh_sphere_omp.cpp
index a32f0f8b51..64bc536bb0 100644
--- a/src/USER-OMP/fix_nh_sphere_omp.cpp
+++ b/src/USER-OMP/fix_nh_sphere_omp.cpp
@@ -15,12 +15,9 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "fix_nh_sphere_omp.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "compute.h"
-#include "group.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/fix_nve_omp.cpp b/src/USER-OMP/fix_nve_omp.cpp
index c61ad7155c..61ed82b16f 100644
--- a/src/USER-OMP/fix_nve_omp.cpp
+++ b/src/USER-OMP/fix_nve_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "fix_nve_omp.h"
 #include "atom.h"
-#include "force.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/USER-OMP/fix_nve_sphere_omp.cpp
index 2286120bee..ccdd654874 100644
--- a/src/USER-OMP/fix_nve_sphere_omp.cpp
+++ b/src/USER-OMP/fix_nve_sphere_omp.cpp
@@ -11,16 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_sphere_omp.h"
+#include <cmath>
 #include "atom.h"
-#include "atom_vec.h"
-#include "update.h"
-#include "respa.h"
 #include "force.h"
-#include "error.h"
 #include "math_vector.h"
 #include "math_extra.h"
 
diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp
index e439647c12..208dfb9432 100644
--- a/src/USER-OMP/fix_nvt_sllod_omp.cpp
+++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp
@@ -15,18 +15,17 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
 #include "fix_nvt_sllod_omp.h"
+#include <cstring>
 #include "math_extra.h"
 #include "atom.h"
-#include "domain.h"
 #include "group.h"
 #include "modify.h"
 #include "fix.h"
 #include "fix_deform.h"
 #include "compute.h"
 #include "error.h"
+#include "domain.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp
index a4587b1c14..1fca1e739b 100644
--- a/src/USER-OMP/fix_omp.cpp
+++ b/src/USER-OMP/fix_omp.cpp
@@ -24,13 +24,10 @@
 #include "neigh_request.h"
 #include "universe.h"
 #include "update.h"
-#include "integrate.h"
-#include "min.h"
 #include "timer.h"
 
 #include "fix_omp.h"
 #include "thr_data.h"
-#include "thr_omp.h"
 
 #include "pair_hybrid.h"
 #include "bond_hybrid.h"
@@ -40,8 +37,11 @@
 #include "kspace.h"
 
 #include <cstring>
-#include <cstdlib>
-#include <cstdio>
+
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
+
 
 #include "suffix.h"
 
diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp
index 2f0a90a790..b0573dfa97 100644
--- a/src/USER-OMP/fix_qeq_comb_omp.cpp
+++ b/src/USER-OMP/fix_qeq_comb_omp.cpp
@@ -15,24 +15,20 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
+#include "fix_qeq_comb_omp.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include "fix_qeq_comb_omp.h"
-#include "fix_omp.h"
+#include "pair_comb.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "group.h"
 #include "memory.h"
-#include "modify.h"
 #include "error.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "respa.h"
 #include "update.h"
-#include "pair_comb_omp.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp
index 45da91305d..f7945b5579 100644
--- a/src/USER-OMP/fix_qeq_reax_omp.cpp
+++ b/src/USER-OMP/fix_qeq_reax_omp.cpp
@@ -31,26 +31,22 @@
    High Performance Computing Applications, to appear.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "fix_qeq_reax_omp.h"
-#include "pair_reaxc_omp.h"
+#include <mpi.h>
+#include <cmath>
+#include "pair_reaxc.h"
 #include "atom.h"
 #include "comm.h"
-#include "domain.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "update.h"
-#include "force.h"
-#include "group.h"
-#include "pair.h"
-#include "respa.h"
 #include "memory.h"
 #include "error.h"
 #include "reaxc_defs.h"
+#include "reaxc_types.h"
+
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp
index 53d0134741..74b2a92775 100644
--- a/src/USER-OMP/fix_rigid_nh_omp.cpp
+++ b/src/USER-OMP/fix_rigid_nh_omp.cpp
@@ -16,7 +16,8 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_rigid_nh_omp.h"
-
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
 #include "atom_vec_line.h"
@@ -24,12 +25,12 @@
 #include "comm.h"
 #include "compute.h"
 #include "domain.h"
+#include "error.h"
 #include "force.h"
 #include "kspace.h"
 #include "modify.h"
 #include "update.h"
-
-#include <cstring>
+#include "timer.h"
 
 #if defined(_OPENMP)
 #include <omp.h>
diff --git a/src/USER-OMP/fix_rigid_nph_omp.cpp b/src/USER-OMP/fix_rigid_nph_omp.cpp
index 7db45ed9bf..31d53868c8 100644
--- a/src/USER-OMP/fix_rigid_nph_omp.cpp
+++ b/src/USER-OMP/fix_rigid_nph_omp.cpp
@@ -17,9 +17,8 @@
                Miller et al., J Chem Phys. 116, 8649-8659 (2002)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_rigid_nph_omp.h"
-#include "domain.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/USER-OMP/fix_rigid_npt_omp.cpp b/src/USER-OMP/fix_rigid_npt_omp.cpp
index a041706f38..1e7c139d52 100644
--- a/src/USER-OMP/fix_rigid_npt_omp.cpp
+++ b/src/USER-OMP/fix_rigid_npt_omp.cpp
@@ -17,9 +17,8 @@
                Miller et al., J Chem Phys. 116, 8649-8659 (2002)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_rigid_npt_omp.h"
-#include "domain.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp
index 12c6362ed8..b807ddba7c 100644
--- a/src/USER-OMP/fix_rigid_omp.cpp
+++ b/src/USER-OMP/fix_rigid_omp.cpp
@@ -16,16 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_rigid_omp.h"
-
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
 #include "atom_vec_line.h"
 #include "atom_vec_tri.h"
 #include "comm.h"
+#include "error.h"
 #include "domain.h"
 
-#include <cstring>
-
 #if defined(_OPENMP)
 #include <omp.h>
 #endif
diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp
index a0495b3b93..41f6c53e40 100644
--- a/src/USER-OMP/fix_rigid_small_omp.cpp
+++ b/src/USER-OMP/fix_rigid_small_omp.cpp
@@ -16,15 +16,14 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_rigid_small_omp.h"
-
+#include <cmath>
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
 #include "atom_vec_line.h"
 #include "atom_vec_tri.h"
 #include "comm.h"
 #include "domain.h"
-
-#include <cstring>
+#include "timer.h"
 
 #if defined(_OPENMP)
 #include <omp.h>
diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp
index c2b493f425..3bff179b44 100644
--- a/src/USER-OMP/improper_class2_omp.cpp
+++ b/src/USER-OMP/improper_class2_omp.cpp
@@ -20,7 +20,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp
index 3b328e5b78..0f99f2732f 100644
--- a/src/USER-OMP/improper_cossq_omp.cpp
+++ b/src/USER-OMP/improper_cossq_omp.cpp
@@ -20,7 +20,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp
index fe1fc45bec..fdc29c74b1 100644
--- a/src/USER-OMP/improper_cvff_omp.cpp
+++ b/src/USER-OMP/improper_cvff_omp.cpp
@@ -20,7 +20,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp
index b5af428cb9..b49b895c78 100644
--- a/src/USER-OMP/improper_fourier_omp.cpp
+++ b/src/USER-OMP/improper_fourier_omp.cpp
@@ -20,7 +20,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp
index 6e02d0968e..32e837fdfe 100644
--- a/src/USER-OMP/improper_harmonic_omp.cpp
+++ b/src/USER-OMP/improper_harmonic_omp.cpp
@@ -20,7 +20,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp
index e198b99337..c8fe685faa 100644
--- a/src/USER-OMP/improper_ring_omp.cpp
+++ b/src/USER-OMP/improper_ring_omp.cpp
@@ -15,15 +15,13 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "improper_ring_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
-#include "update.h"
-#include "error.h"
 #include "math_special.h"
 
 #include "suffix.h"
diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp
index ceaca35074..f3fdf4570f 100644
--- a/src/USER-OMP/improper_umbrella_omp.cpp
+++ b/src/USER-OMP/improper_umbrella_omp.cpp
@@ -20,7 +20,7 @@
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "domain.h"
+#include "timer.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp
index 8a920e05d5..3c5439db5d 100644
--- a/src/USER-OMP/msm_cg_omp.cpp
+++ b/src/USER-OMP/msm_cg_omp.cpp
@@ -16,10 +16,10 @@
    Original MSM class by: Paul Crozier, Stan Moore, Stephen Bond, (all SNL)
 ------------------------------------------------------------------------- */
 
+#include "msm_cg_omp.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
 #include <cstring>
 
 #include "atom.h"
@@ -29,12 +29,14 @@
 #include "force.h"
 #include "neighbor.h"
 #include "memory.h"
-#include "msm_cg_omp.h"
+#include "thr_omp.h"
+#include "timer.h"
 
-#include "math_const.h"
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define OFFSET 16384
 #define SMALLQ 0.00001
diff --git a/src/USER-OMP/msm_omp.cpp b/src/USER-OMP/msm_omp.cpp
index 74cbb56be7..81f84e8f6f 100644
--- a/src/USER-OMP/msm_omp.cpp
+++ b/src/USER-OMP/msm_omp.cpp
@@ -16,15 +16,11 @@
 ------------------------------------------------------------------------- */
 
 #include "msm_omp.h"
-#include "atom.h"
+#include <cstring>
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "force.h"
-#include "memory.h"
-#include "math_const.h"
-
-#include <cstring>
+#include "timer.h"
 
 #if defined(_OPENMP)
 #include <omp.h>
diff --git a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp
index d9e0fb9297..3bda2e4c5a 100644
--- a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp
+++ b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp
@@ -13,16 +13,13 @@
 
 #include "npair_full_bin_atomonly_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "domain.h"
 #include "my_page.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace NeighConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/USER-OMP/npair_full_bin_ghost_omp.cpp b/src/USER-OMP/npair_full_bin_ghost_omp.cpp
index b915aca002..b0b0070df5 100644
--- a/src/USER-OMP/npair_full_bin_ghost_omp.cpp
+++ b/src/USER-OMP/npair_full_bin_ghost_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_full_bin_ghost_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
@@ -23,7 +22,6 @@
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace NeighConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/USER-OMP/npair_full_bin_omp.cpp b/src/USER-OMP/npair_full_bin_omp.cpp
index e1f75c06e2..d3e30b4932 100644
--- a/src/USER-OMP/npair_full_bin_omp.cpp
+++ b/src/USER-OMP/npair_full_bin_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_full_bin_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
@@ -23,7 +22,6 @@
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace NeighConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp
index 9bc196e17a..707db2edcf 100644
--- a/src/USER-OMP/npair_full_multi_omp.cpp
+++ b/src/USER-OMP/npair_full_multi_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_full_multi_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
@@ -23,7 +22,6 @@
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace NeighConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/USER-OMP/npair_full_nsq_ghost_omp.cpp b/src/USER-OMP/npair_full_nsq_ghost_omp.cpp
index b33f76bb22..527df58fd6 100644
--- a/src/USER-OMP/npair_full_nsq_ghost_omp.cpp
+++ b/src/USER-OMP/npair_full_nsq_ghost_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_full_nsq_ghost_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
@@ -23,7 +22,6 @@
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace NeighConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/USER-OMP/npair_full_nsq_omp.cpp b/src/USER-OMP/npair_full_nsq_omp.cpp
index 1d0f26d638..2719f5dc2c 100644
--- a/src/USER-OMP/npair_full_nsq_omp.cpp
+++ b/src/USER-OMP/npair_full_nsq_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_full_nsq_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
@@ -24,7 +23,6 @@
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace NeighConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp
index 02d98ff6ab..a69779d96d 100644
--- a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp
@@ -13,12 +13,9 @@
 
 #include "npair_half_bin_atomonly_newton_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
 #include "my_page.h"
 #include "error.h"
 
diff --git a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp
index 24fe75ec55..5f8ffdab29 100644
--- a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp
+++ b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_bin_newtoff_ghost_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_bin_newtoff_omp.cpp
index ff74b54d7d..35807645cf 100644
--- a/src/USER-OMP/npair_half_bin_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_bin_newtoff_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_bin_newtoff_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_bin_newton_omp.cpp b/src/USER-OMP/npair_half_bin_newton_omp.cpp
index f7d969ba27..2700d6863b 100644
--- a/src/USER-OMP/npair_half_bin_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_bin_newton_omp.cpp
@@ -13,11 +13,9 @@
 
 #include "npair_half_bin_newton_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "group.h"
 #include "molecule.h"
 #include "domain.h"
 #include "my_page.h"
diff --git a/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp
index c843d623cd..d94845898c 100644
--- a/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp
+++ b/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_bin_newton_tri_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp
index 705d1b8d9f..c06737dc1c 100644
--- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_multi_newtoff_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp
index f16dd027a0..50df756be4 100644
--- a/src/USER-OMP/npair_half_multi_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_multi_newton_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp
index ce93e85485..8b78b311dd 100644
--- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp
+++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_multi_newton_tri_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp
index add4c44d9e..f0eb211425 100644
--- a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp
+++ b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_nsq_newtoff_ghost_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp
index 01da73cf1e..55b9f9e512 100644
--- a/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_nsq_newtoff_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_nsq_newton_omp.cpp
index 3815b1b85b..223da622e8 100644
--- a/src/USER-OMP/npair_half_nsq_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_nsq_newton_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_nsq_newton_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp
index f094691b71..9bb4d277fe 100644
--- a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_respa_bin_newtoff_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp
index de7ef5f7d5..9ed0ae482d 100644
--- a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_respa_bin_newton_omp.h"
-#include "neighbor.h"
 #include "npair_omp.h"
 #include "neigh_list.h"
 #include "atom.h"
diff --git a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp
index f20d101bc9..cd03684940 100644
--- a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp
+++ b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_respa_bin_newton_tri_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp
index 0f726cdd7f..b1e7467ec7 100644
--- a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_respa_nsq_newtoff_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp
index 2783e1255e..c22965895d 100644
--- a/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_respa_nsq_newton_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
index dff2a762d5..1b437482c4 100644
--- a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
@@ -11,10 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "npair_half_size_bin_newtoff_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
index 3053b81594..8e0581d4ce 100644
--- a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
@@ -11,10 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "npair_half_size_bin_newton_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
index b02bfa345e..38a2c0d61f 100644
--- a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
@@ -13,7 +13,6 @@
 
 #include "npair_half_size_bin_newton_tri_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
index 717012b226..d1505e1b2e 100644
--- a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
@@ -11,10 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "npair_half_size_nsq_newtoff_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
index 5a55029d30..9027b0728d 100644
--- a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
@@ -11,10 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "npair_half_size_nsq_newton_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.cpp b/src/USER-OMP/npair_halffull_newtoff_omp.cpp
index 947e4e1ad2..7d2fe4f109 100644
--- a/src/USER-OMP/npair_halffull_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_halffull_newtoff_omp.cpp
@@ -13,12 +13,8 @@
 
 #include "npair_halffull_newtoff_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "atom.h"
 #include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
 #include "my_page.h"
 #include "error.h"
 
diff --git a/src/USER-OMP/npair_halffull_newton_omp.cpp b/src/USER-OMP/npair_halffull_newton_omp.cpp
index 6e158d372d..3fcc8c2e98 100644
--- a/src/USER-OMP/npair_halffull_newton_omp.cpp
+++ b/src/USER-OMP/npair_halffull_newton_omp.cpp
@@ -13,12 +13,9 @@
 
 #include "npair_halffull_newton_omp.h"
 #include "npair_omp.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
 #include "my_page.h"
 #include "error.h"
 
diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp
index 90c3777932..8d0605fae9 100644
--- a/src/USER-OMP/pair_beck_omp.cpp
+++ b/src/USER-OMP/pair_beck_omp.cpp
@@ -12,14 +12,14 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_beck_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "math_special.h"
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp
index 567eddc9cb..55da972c4e 100644
--- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp
+++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp
@@ -12,14 +12,14 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_born_coul_wolf_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "math_const.h"
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp
index fce2013745..35ad4fcb48 100644
--- a/src/USER-OMP/pair_born_omp.cpp
+++ b/src/USER-OMP/pair_born_omp.cpp
@@ -12,13 +12,13 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_born_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp
index cef9fb0955..6367976c7d 100644
--- a/src/USER-OMP/pair_brownian_omp.cpp
+++ b/src/USER-OMP/pair_brownian_omp.cpp
@@ -12,8 +12,8 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_brownian_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
@@ -26,6 +26,7 @@
 #include "random_mars.h"
 #include "math_const.h"
 #include "math_special.h"
+#include "timer.h"
 
 #include "fix_wall.h"
 
diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp
index 239a820242..dcb4124634 100644
--- a/src/USER-OMP/pair_brownian_poly_omp.cpp
+++ b/src/USER-OMP/pair_brownian_poly_omp.cpp
@@ -12,8 +12,8 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_brownian_poly_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp
index cc7e81b9c5..8d5c80513a 100644
--- a/src/USER-OMP/pair_buck_omp.cpp
+++ b/src/USER-OMP/pair_buck_omp.cpp
@@ -12,13 +12,13 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_buck_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp
index 056daf210a..267beeecbd 100644
--- a/src/USER-OMP/pair_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_coul_cut_omp.cpp
@@ -12,13 +12,13 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_coul_cut_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp
index d202e314bf..4d3f92c495 100644
--- a/src/USER-OMP/pair_coul_debye_omp.cpp
+++ b/src/USER-OMP/pair_coul_debye_omp.cpp
@@ -12,13 +12,13 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_coul_debye_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/USER-OMP/pair_coul_dsf_omp.cpp
index 217fb844c3..bd7f5cfed2 100644
--- a/src/USER-OMP/pair_coul_dsf_omp.cpp
+++ b/src/USER-OMP/pair_coul_dsf_omp.cpp
@@ -12,14 +12,13 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_coul_dsf_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-
+#include "timer.h"
 #include "suffix.h"
 #include "math_const.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp
index 0913a2b188..92d5bd7b15 100644
--- a/src/USER-OMP/pair_coul_wolf_omp.cpp
+++ b/src/USER-OMP/pair_coul_wolf_omp.cpp
@@ -12,14 +12,14 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_coul_wolf_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "math_const.h"
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp
index 77db3d9183..b7f3a7f4d4 100644
--- a/src/USER-OMP/pair_dpd_omp.cpp
+++ b/src/USER-OMP/pair_dpd_omp.cpp
@@ -12,15 +12,15 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_dpd_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "update.h"
 #include "random_mars.h"
+#include "timer.h"
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
index 85cab4fe7b..87d637e80d 100644
--- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
@@ -15,13 +15,15 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_lj_cut_thole_long_omp.h"
 #include <cmath>
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_lj_cut_thole_long_omp.h"
 #include "atom.h"
 #include "comm.h"
+#include "domain.h"
+#include "fix_drude.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
@@ -29,7 +31,7 @@
 #include "math_const.h"
 #include "error.h"
 #include "suffix.h"
-#include "domain.h"
+#include "timer.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
index e2c1da1a89..18fc207015 100644
--- a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
@@ -12,8 +12,8 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_lj_cut_tip4p_long_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "domain.h"
 #include "comm.h"
diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp
index 3a5f03364d..04ac59b121 100644
--- a/src/USER-OMP/pair_lubricate_poly_omp.cpp
+++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp
@@ -12,8 +12,8 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_lubricate_poly_omp.h"
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp
index 2f17515130..aedd438066 100644
--- a/src/USER-OMP/pair_reaxc_omp.cpp
+++ b/src/USER-OMP/pair_reaxc_omp.cpp
@@ -34,6 +34,8 @@
  ------------------------------------------------------------------------- */
 
 #include "pair_reaxc_omp.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
@@ -42,32 +44,27 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "modify.h"
-#include "fix.h"
 #include "fix_reaxc.h"
 #include "citeme.h"
 #include "memory.h"
 #include "error.h"
 #include "timer.h"
 
+#include "reaxc_defs.h"
 #include "reaxc_types.h"
 #include "reaxc_allocate.h"
-#include "reaxc_control.h"
-#include "reaxc_ffield.h"
 #include "reaxc_forces_omp.h"
 #include "reaxc_init_md_omp.h"
 #include "reaxc_io_tools.h"
 #include "reaxc_list.h"
-#include "reaxc_lookup.h"
 #include "reaxc_reset_tools.h"
 #include "reaxc_tool_box.h"
-#include "reaxc_traj.h"
-#include "reaxc_vector.h"
-#include "fix_reaxc_bonds.h"
 
 #if defined(_OPENMP)
 #include <omp.h>
 #endif
 
+#include "suffix.h"
 using namespace LAMMPS_NS;
 
 #ifdef OMP_TIMING
diff --git a/src/USER-OMP/pair_reaxc_omp.h b/src/USER-OMP/pair_reaxc_omp.h
index ad8c368aaf..0cae28f56b 100644
--- a/src/USER-OMP/pair_reaxc_omp.h
+++ b/src/USER-OMP/pair_reaxc_omp.h
@@ -22,7 +22,6 @@ PairStyle(reax/c/omp,PairReaxCOMP)
 
 #include "pair_reaxc.h"
 #include "thr_omp.h"
-#include "suffix.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp
index 2b4619f685..1117979f1f 100644
--- a/src/USER-OMP/pppm_cg_omp.cpp
+++ b/src/USER-OMP/pppm_cg_omp.cpp
@@ -15,20 +15,20 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
+#include "pppm_cg_omp.h"
+#include <mpi.h>
 #include <cstring>
 #include <cmath>
-#include "pppm_cg_omp.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "error.h"
-#include "fix_omp.h"
 #include "force.h"
-#include "neighbor.h"
-#include "memory.h"
 #include "math_const.h"
 #include "math_special.h"
-
+#include "timer.h"
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
 #include "suffix.h"
 using namespace LAMMPS_NS;
 using namespace MathConst;
diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp
index 435341a31c..de902b1a57 100644
--- a/src/USER-OMP/pppm_disp_omp.cpp
+++ b/src/USER-OMP/pppm_disp_omp.cpp
@@ -16,15 +16,20 @@
                          Rolf Isele-Holder (RWTH Aachen University)
 ------------------------------------------------------------------------- */
 
+#include "pppm_disp_omp.h"
+#include <mpi.h>
 #include <cstring>
 #include <cmath>
-#include "pppm_disp_omp.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
+#include "error.h"
 #include "force.h"
-#include "memory.h"
 #include "math_const.h"
+#include "timer.h"
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp
index a53c5b2ac5..fc9466e395 100644
--- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp
+++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp
@@ -15,23 +15,22 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
+#include "pppm_disp_tip4p_omp.h"
+#include <mpi.h>
 #include <cstring>
 #include <cmath>
-#include "pppm_disp_tip4p_omp.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_omp.h"
 #include "force.h"
-#include "memory.h"
 #include "math_const.h"
-#include "math_special.h"
-
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
 #include "suffix.h"
 using namespace LAMMPS_NS;
 using namespace MathConst;
-using namespace MathSpecial;
 
 #ifdef FFT_SINGLE
 #define ZEROF 0.0f
diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp
index 66190b3f51..3ef3de1ab7 100644
--- a/src/USER-OMP/pppm_omp.cpp
+++ b/src/USER-OMP/pppm_omp.cpp
@@ -15,18 +15,21 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
+#include "pppm_omp.h"
+#include <mpi.h>
 #include <cstring>
 #include <cmath>
-#include "pppm_omp.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "error.h"
-#include "fix_omp.h"
 #include "force.h"
-#include "memory.h"
 #include "math_const.h"
 #include "math_special.h"
+#include "timer.h"
+
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp
index 5fe44d2b71..d7c12613d9 100644
--- a/src/USER-OMP/pppm_tip4p_omp.cpp
+++ b/src/USER-OMP/pppm_tip4p_omp.cpp
@@ -15,18 +15,21 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
+#include "pppm_tip4p_omp.h"
+#include <mpi.h>
 #include <cstring>
 #include <cmath>
-#include "pppm_tip4p_omp.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_omp.h"
 #include "force.h"
-#include "memory.h"
 #include "math_const.h"
 #include "math_special.h"
+#include "timer.h"
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
 
 #include "suffix.h"
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp
index 33780f5e3f..d581819e00 100644
--- a/src/USER-OMP/reaxc_bond_orders_omp.cpp
+++ b/src/USER-OMP/reaxc_bond_orders_omp.cpp
@@ -26,9 +26,13 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
+#include "reaxc_bond_orders_omp.h"
+#include <mpi.h>
+#include <cmath>
+#include "fix_omp.h"
+#include "reaxc_defs.h"
 #include "pair_reaxc_omp.h"
 #include "reaxc_types.h"
-#include "reaxc_bond_orders_omp.h"
 #include "reaxc_list.h"
 #include "reaxc_vector.h"
 
diff --git a/src/USER-OMP/reaxc_bonds_omp.cpp b/src/USER-OMP/reaxc_bonds_omp.cpp
index 5160c6f55d..b6a76b3f3a 100644
--- a/src/USER-OMP/reaxc_bonds_omp.cpp
+++ b/src/USER-OMP/reaxc_bonds_omp.cpp
@@ -26,13 +26,13 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc_omp.h"
-
 #include "reaxc_bonds_omp.h"
-#include "reaxc_bond_orders_omp.h"
+#include <mpi.h>
+#include <cmath>
+#include "fix_omp.h"
+#include "reaxc_defs.h"
+#include "pair_reaxc_omp.h"
 #include "reaxc_list.h"
-#include "reaxc_tool_box.h"
-#include "reaxc_vector.h"
 
 #if defined(_OPENMP)
 #include  <omp.h>
diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp
index 0a08bd6a46..971667cc2d 100644
--- a/src/USER-OMP/reaxc_forces_omp.cpp
+++ b/src/USER-OMP/reaxc_forces_omp.cpp
@@ -26,19 +26,19 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc_omp.h"
-#include "thr_data.h"
-
 #include "reaxc_forces_omp.h"
+#include <mpi.h>
+#include <cmath>
+#include "fix_omp.h"
+#include "reaxc_defs.h"
+#include "pair_reaxc_omp.h"
+
 #include "reaxc_bond_orders_omp.h"
 #include "reaxc_bonds_omp.h"
 #include "reaxc_hydrogen_bonds_omp.h"
-#include "reaxc_io_tools.h"
 #include "reaxc_list.h"
-#include "reaxc_lookup.h"
 #include "reaxc_multi_body_omp.h"
 #include "reaxc_nonbonded_omp.h"
-#include "reaxc_tool_box.h"
 #include "reaxc_torsion_angles_omp.h"
 #include "reaxc_valence_angles_omp.h"
 #include "reaxc_vector.h"
diff --git a/src/USER-OMP/reaxc_forces_omp.h b/src/USER-OMP/reaxc_forces_omp.h
index d1e2a5c65a..6df0288656 100644
--- a/src/USER-OMP/reaxc_forces_omp.h
+++ b/src/USER-OMP/reaxc_forces_omp.h
@@ -30,7 +30,6 @@
 #define __FORCES_OMP_H_
 
 #include "reaxc_types.h"
-#include "reaxc_defs.h"
 
 void Init_Force_FunctionsOMP( control_params* );
 void Compute_ForcesOMP( reax_system*, control_params*, simulation_data*,
diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
index 7acf26262e..d06966a92d 100644
--- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
+++ b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
@@ -26,10 +26,12 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc_omp.h"
-
 #include "reaxc_hydrogen_bonds_omp.h"
-#include "reaxc_bond_orders_omp.h"
+#include <mpi.h>
+#include <cmath>
+#include "fix_omp.h"
+#include "pair_reaxc_omp.h"
+#include "reaxc_defs.h"
 #include "reaxc_list.h"
 #include "reaxc_valence_angles.h"     // To access Calculate_Theta()
 #include "reaxc_valence_angles_omp.h" // To access Calculate_dCos_ThetaOMP()
diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp
index fe7682d035..9d40479ddf 100644
--- a/src/USER-OMP/reaxc_init_md_omp.cpp
+++ b/src/USER-OMP/reaxc_init_md_omp.cpp
@@ -26,18 +26,16 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc_omp.h"
 #include "reaxc_init_md_omp.h"
-#include "reaxc_allocate.h"
+#include <cstdlib>
+#include "reaxc_defs.h"
 #include "reaxc_forces.h"
 #include "reaxc_forces_omp.h"
 #include "reaxc_io_tools.h"
 #include "reaxc_list.h"
 #include "reaxc_lookup.h"
-#include "reaxc_reset_tools.h"
-#include "reaxc_system_props.h"
 #include "reaxc_tool_box.h"
-#include "reaxc_vector.h"
+#include "error.h"
 
 // Functions defined in reaxc_init_md.cpp
 extern int Init_MPI_Datatypes(reax_system*, storage*, mpi_datatypes*, MPI_Comm, char*);
diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp
index 7552e7a733..5f4b6d4eb0 100644
--- a/src/USER-OMP/reaxc_multi_body_omp.cpp
+++ b/src/USER-OMP/reaxc_multi_body_omp.cpp
@@ -26,13 +26,14 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc_omp.h"
-#include "thr_data.h"
-
 #include "reaxc_multi_body_omp.h"
-#include "reaxc_bond_orders_omp.h"
+#include <mpi.h>
+#include <cmath>
+#include "fix_omp.h"
+#include <cstring>
+#include "pair_reaxc_omp.h"
+#include "reaxc_defs.h"
 #include "reaxc_list.h"
-#include "reaxc_vector.h"
 
 #if defined(_OPENMP)
 #include  <omp.h>
diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/USER-OMP/reaxc_nonbonded_omp.cpp
index ea92e0c210..564088880a 100644
--- a/src/USER-OMP/reaxc_nonbonded_omp.cpp
+++ b/src/USER-OMP/reaxc_nonbonded_omp.cpp
@@ -29,6 +29,7 @@
 #include "pair_reaxc_omp.h"
 #include "thr_data.h"
 
+#include "reaxc_defs.h"
 #include "reaxc_types.h"
 
 #include "reaxc_nonbonded.h"
diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/USER-OMP/reaxc_torsion_angles_omp.cpp
index d290dc264f..68bacb7202 100644
--- a/src/USER-OMP/reaxc_torsion_angles_omp.cpp
+++ b/src/USER-OMP/reaxc_torsion_angles_omp.cpp
@@ -26,14 +26,14 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc_omp.h"
-#include "thr_data.h"
-
-#include "reaxc_types.h"
 #include "reaxc_torsion_angles_omp.h"
-#include "reaxc_bond_orders_omp.h"
+#include <mpi.h>
+#include "fix_omp.h"
+#include "pair_reaxc_omp.h"
+
+#include "reaxc_defs.h"
+#include "reaxc_types.h"
 #include "reaxc_list.h"
-#include "reaxc_tool_box.h"
 #include "reaxc_vector.h"
 
 #if defined(_OPENMP)
diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/USER-OMP/reaxc_valence_angles_omp.cpp
index 195f16a75d..104fadbbae 100644
--- a/src/USER-OMP/reaxc_valence_angles_omp.cpp
+++ b/src/USER-OMP/reaxc_valence_angles_omp.cpp
@@ -26,13 +26,16 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
+#include "reaxc_valence_angles_omp.h"
+#include <mpi.h>
+#include <cmath>
 #include "pair_reaxc_omp.h"
-#include "thr_data.h"
+#include "fix_omp.h"
+#include "error.h"
 
+#include "reaxc_defs.h"
 #include "reaxc_types.h"
 #include "reaxc_valence_angles.h"
-#include "reaxc_valence_angles_omp.h"
-#include "reaxc_bond_orders_omp.h"
 #include "reaxc_list.h"
 #include "reaxc_vector.h"
 
diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp
index 9c8555c66d..5add419253 100644
--- a/src/USER-OMP/respa_omp.cpp
+++ b/src/USER-OMP/respa_omp.cpp
@@ -15,13 +15,11 @@
    Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "respa_omp.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "atom.h"
+#include "domain.h"
 #include "force.h"
 #include "pair.h"
 #include "bond.h"
@@ -32,11 +30,8 @@
 #include "output.h"
 #include "update.h"
 #include "modify.h"
-#include "compute.h"
-#include "fix_respa.h"
-#include "timer.h"
-#include "memory.h"
 #include "error.h"
+#include "timer.h"
 
 #if defined(_OPENMP)
 #include <omp.h>
diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h
index 3cea1b0018..68673e7503 100644
--- a/src/USER-OMP/thr_data.h
+++ b/src/USER-OMP/thr_data.h
@@ -18,10 +18,6 @@
 #ifndef LMP_THR_DATA_H
 #define LMP_THR_DATA_H
 
-#if defined(_OPENMP)
-#include <omp.h>
-#endif
-
 #include "timer.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-OMP/thr_omp.cpp b/src/USER-OMP/thr_omp.cpp
index 22f751e6c0..51030358d3 100644
--- a/src/USER-OMP/thr_omp.cpp
+++ b/src/USER-OMP/thr_omp.cpp
@@ -22,7 +22,6 @@
 #include "comm.h"
 #include "error.h"
 #include "force.h"
-#include "memory.h"
 #include "modify.h"
 #include "neighbor.h"
 #include "timer.h"
@@ -34,7 +33,6 @@
 #include "angle.h"
 #include "dihedral.h"
 #include "improper.h"
-#include "kspace.h"
 #include "compute.h"
 
 #include "math_const.h"
diff --git a/src/USER-OMP/thr_omp.h b/src/USER-OMP/thr_omp.h
index 87d921290e..062d77bc0e 100644
--- a/src/USER-OMP/thr_omp.h
+++ b/src/USER-OMP/thr_omp.h
@@ -18,10 +18,13 @@
 #ifndef LMP_THR_OMP_H
 #define LMP_THR_OMP_H
 
+#if defined(_OPENMP)
+#include <omp.h>
+#endif
 #include "pointers.h"
 #include "error.h"
-#include "fix_omp.h"
-#include "thr_data.h"
+#include "fix_omp.h"  // IWYU pragma: export
+#include "thr_data.h" // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
@@ -31,8 +34,6 @@ class Bond;
 class Angle;
 class Dihedral;
 class Improper;
-class KSpace;
-class Fix;
 
 class ThrOMP {
 
diff --git a/src/USER-PHONON/Install.sh b/src/USER-PHONON/Install.sh
index a73f529cfa..26104b45cf 100755
--- a/src/USER-PHONON/Install.sh
+++ b/src/USER-PHONON/Install.sh
@@ -42,5 +42,3 @@ action fix_phonon.cpp fft3d_wrap.h
 action fix_phonon.h fft3d_wrap.h
 action dynamical_matrix.cpp
 action dynamical_matrix.h
-action third_order.cpp
-action third_order.h
diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp
index d94bd11a80..559ef4c36f 100644
--- a/src/USER-PHONON/dynamical_matrix.cpp
+++ b/src/USER-PHONON/dynamical_matrix.cpp
@@ -3,15 +3,15 @@
 //
 
 #include <mpi.h>
-#include <cstdlib>
+#include <cmath>
+#include <cstring>
 #include "dynamical_matrix.h"
 #include "atom.h"
-#include "modify.h"
 #include "domain.h"
 #include "comm.h"
+#include "error.h"
 #include "group.h"
 #include "force.h"
-#include "math_extra.h"
 #include "memory.h"
 #include "bond.h"
 #include "angle.h"
@@ -25,7 +25,6 @@
 #include "finish.h"
 #include <algorithm>
 
-
 using namespace LAMMPS_NS;
 enum{REGULAR,ESKM};
 
diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp
index cdbe4068bc..9b663ce383 100644
--- a/src/USER-PHONON/fix_phonon.cpp
+++ b/src/USER-PHONON/fix_phonon.cpp
@@ -23,8 +23,8 @@
      konglt@sjtu.edu.cn; konglt@gmail.com
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
+#include <mpi.h>
+#include <cmath>
 #include <cstring>
 #include "fix_phonon.h"
 #include "fft3d_wrap.h"
@@ -33,7 +33,6 @@
 #include "domain.h"
 #include "force.h"
 #include "group.h"
-#include "lattice.h"
 #include "modify.h"
 #include "update.h"
 #include "citeme.h"
diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/USER-PLUMED/fix_plumed.cpp
index 8bd0ecca05..c75a48f9b4 100644
--- a/src/USER-PLUMED/fix_plumed.cpp
+++ b/src/USER-PLUMED/fix_plumed.cpp
@@ -107,7 +107,11 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
   // whereas if partitions are not defined then world is equal to
   // MPI_COMM_WORLD.
 
+#if !defined(MPI_STUBS)
+  // plumed does not know about LAMMPS using the MPI STUBS library and will
+  // fail if this is called under these circumstances
   p->cmd("setMPIComm",&world);
+#endif
 
   // Set up units
   // LAMMPS units wrt kj/mol - nm - ps
diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp
index 41e6540b97..ad3d3facdb 100644
--- a/src/USER-PTM/compute_ptm_atom.cpp
+++ b/src/USER-PTM/compute_ptm_atom.cpp
@@ -16,15 +16,14 @@ under
          Contributing author: PM Larsen (MIT)
 ------------------------------------------------------------------------- */
 
+#include "compute_ptm_atom.h"
 #include <algorithm>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
 #include <vector>
 
 #include "atom.h"
 #include "comm.h"
-#include "compute_ptm_atom.h"
 #include "error.h"
 #include "force.h"
 #include "memory.h"
@@ -32,7 +31,6 @@ under
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "neighbor.h"
-#include "pair.h"
 #include "update.h"
 
 #include "ptm_functions.h"
diff --git a/src/USER-PTM/ptm_convex_hull_incremental.cpp b/src/USER-PTM/ptm_convex_hull_incremental.cpp
index 45643ec515..8dd06e8168 100644
--- a/src/USER-PTM/ptm_convex_hull_incremental.cpp
+++ b/src/USER-PTM/ptm_convex_hull_incremental.cpp
@@ -11,7 +11,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #include <cfloat>
 #include <cstring>
 #include <cassert>
-#include <algorithm>
 #include "ptm_convex_hull_incremental.h"
 #include "ptm_constants.h"
 
diff --git a/src/USER-PTM/ptm_index.cpp b/src/USER-PTM/ptm_index.cpp
index 3068e7a7f6..cedd35126d 100644
--- a/src/USER-PTM/ptm_index.cpp
+++ b/src/USER-PTM/ptm_index.cpp
@@ -12,20 +12,17 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #include "ptm_convex_hull_incremental.h"
 #include "ptm_deformation_gradient.h"
 #include "ptm_functions.h"
-#include "ptm_graph_data.h"
 #include "ptm_initialize_data.h"
 #include "ptm_neighbour_ordering.h"
 #include "ptm_normalize_vertices.h"
 #include "ptm_polar.h"
 #include "ptm_quat.h"
 #include "ptm_structure_matcher.h"
-#include <algorithm>
 #include <cassert>
-#include <cfloat>
 #include <cmath>
 #include <cstdio>
-#include <cstdlib>
 #include <cstring>
+#include <stdint.h>
 
 static double calculate_interatomic_distance(int type, double scale) {
         assert(type >= 1 && type <= 8);
diff --git a/src/USER-PTM/ptm_initialize_data.cpp b/src/USER-PTM/ptm_initialize_data.cpp
index 49dc6f2323..ff8245fe44 100644
--- a/src/USER-PTM/ptm_initialize_data.cpp
+++ b/src/USER-PTM/ptm_initialize_data.cpp
@@ -7,14 +7,12 @@ The above copyright notice and this permission notice shall be included in all c
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <cmath>
-#include <cfloat>
-#include <cassert>
-#include <algorithm>
 #include "ptm_initialize_data.h"
+#include "ptm_canonical_coloured.h"
+#include "ptm_convex_hull_incremental.h"
+#include "ptm_graph_tools.h"
+#include "ptm_neighbour_ordering.h"
+#include <cassert>
 
 
 static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3])
diff --git a/src/USER-PTM/ptm_initialize_data.h b/src/USER-PTM/ptm_initialize_data.h
index 20c9921962..87111b1282 100644
--- a/src/USER-PTM/ptm_initialize_data.h
+++ b/src/USER-PTM/ptm_initialize_data.h
@@ -12,13 +12,10 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 
 
 #include "ptm_graph_data.h"
-#include "ptm_graph_tools.h"
 #include "ptm_deformation_gradient.h"
 #include "ptm_fundamental_mappings.h"
-#include "ptm_neighbour_ordering.h"
-#include "ptm_canonical_coloured.h"
-#include "ptm_convex_hull_incremental.h"
 #include "ptm_alt_templates.h"
+#include <cstddef>
 
 
 namespace ptm {
diff --git a/src/USER-PTM/ptm_neighbour_ordering.cpp b/src/USER-PTM/ptm_neighbour_ordering.cpp
index cb72a43711..1332b8819b 100644
--- a/src/USER-PTM/ptm_neighbour_ordering.cpp
+++ b/src/USER-PTM/ptm_neighbour_ordering.cpp
@@ -9,16 +9,15 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 
 //todo: normalize vertices
 
-#include <cstdlib>
+#include "ptm_neighbour_ordering.h"
 #include <cmath>
 #include <cstring>
 #include <cassert>
 #include <algorithm>
 #include <set>
+#include <vector>
 #include "ptm_constants.h"
 #include "ptm_voronoi_cell.h"
-#include "ptm_neighbour_ordering.h"
-#include "ptm_normalize_vertices.h"
 
 
 namespace ptm {
diff --git a/src/USER-PTM/ptm_polar.h b/src/USER-PTM/ptm_polar.h
index e03963048b..f11dd98ee9 100644
--- a/src/USER-PTM/ptm_polar.h
+++ b/src/USER-PTM/ptm_polar.h
@@ -11,7 +11,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #define PTM_POLAR_H
 
 #include <stdint.h>
-#include <stdbool.h>
 
 namespace ptm {
 
diff --git a/src/USER-PTM/ptm_quat.cpp b/src/USER-PTM/ptm_quat.cpp
index 4a93499b3a..527f4d1116 100644
--- a/src/USER-PTM/ptm_quat.cpp
+++ b/src/USER-PTM/ptm_quat.cpp
@@ -7,9 +7,9 @@ The above copyright notice and this permission notice shall be included in all c
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
+#include "ptm_quat.h"
 #include <cstring>
 #include <cmath>
-#include <cfloat>
 #include <algorithm>
 
 
diff --git a/src/USER-PTM/ptm_structure_matcher.cpp b/src/USER-PTM/ptm_structure_matcher.cpp
index d50676a3c1..b587ad225f 100644
--- a/src/USER-PTM/ptm_structure_matcher.cpp
+++ b/src/USER-PTM/ptm_structure_matcher.cpp
@@ -7,20 +7,16 @@ The above copyright notice and this permission notice shall be included in all c
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-#include <cstdio>
-#include <cstdlib>
+#include "ptm_structure_matcher.h"
 #include <cstring>
 #include <cmath>
-#include <cfloat>
-#include <cassert>
-#include <algorithm>
+#include <utility>
 #include "ptm_convex_hull_incremental.h"
 #include "ptm_canonical_coloured.h"
 #include "ptm_graph_data.h"
 #include "ptm_graph_tools.h"
 #include "ptm_normalize_vertices.h"
 #include "ptm_polar.h"
-#include "ptm_structure_matcher.h"
 #include "ptm_constants.h"
 
 
diff --git a/src/USER-PTM/ptm_structure_matcher.h b/src/USER-PTM/ptm_structure_matcher.h
index e75892f8cb..63bc5ed1fe 100644
--- a/src/USER-PTM/ptm_structure_matcher.h
+++ b/src/USER-PTM/ptm_structure_matcher.h
@@ -12,7 +12,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 
 #include "ptm_initialize_data.h"
 #include "ptm_constants.h"
-
+#include "ptm_convex_hull_incremental.h"
 
 namespace ptm {
 
diff --git a/src/USER-PTM/ptm_voronoi_cell.cpp b/src/USER-PTM/ptm_voronoi_cell.cpp
index dfe61eb24f..dc4ce4e747 100644
--- a/src/USER-PTM/ptm_voronoi_cell.cpp
+++ b/src/USER-PTM/ptm_voronoi_cell.cpp
@@ -52,7 +52,7 @@ such enhancements or derivative works thereof, in binary and source code form.
  * \brief Function implementations for the voronoicell and related classes. */
 
 #include <cmath>
-#include <cstring>
+#include <cstdio>
 #include <cstdlib>
 #include "ptm_voronoi_config.h"
 #include "ptm_voronoi_cell.h"
diff --git a/src/USER-PTM/ptm_voronoi_cell.h b/src/USER-PTM/ptm_voronoi_cell.h
index eb091dd36b..69e3b5bdc4 100644
--- a/src/USER-PTM/ptm_voronoi_cell.h
+++ b/src/USER-PTM/ptm_voronoi_cell.h
@@ -56,9 +56,6 @@ such enhancements or derivative works thereof, in binary and source code form.
 #define PTM_VOROPP_CELL_HH
 
 #include <vector>
-#include <cstdio>
-
-#include "ptm_voronoi_config.h"
 
 namespace ptm_voro {
 
diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp
index b9b07664d2..abbf1701b8 100644
--- a/src/USER-QTB/fix_qbmsst.cpp
+++ b/src/USER-QTB/fix_qbmsst.cpp
@@ -16,31 +16,22 @@
    Implementation of the Multi-Scale Shock Method with quantum nuclear effects
 ------------------------------------------------------------------------- */
 
+#include "fix_qbmsst.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
 #include <cstdlib>
-#include "fix_qbmsst.h"
-#include "math_extra.h"
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "force.h"
 #include "update.h"
 #include "modify.h"
 #include "compute.h"
 #include "domain.h"
-#include "region.h"
-#include "respa.h"
 #include "comm.h"
-#include "input.h"
-#include "output.h"
-#include "variable.h"
 #include "random_mars.h"
 #include "memory.h"
 #include "error.h"
-#include "group.h"
 #include "kspace.h"
-#include "thermo.h"
 #include "utils.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp
index 015f953b8e..593ca31006 100644
--- a/src/USER-QTB/fix_qtb.cpp
+++ b/src/USER-QTB/fix_qtb.cpp
@@ -16,28 +16,21 @@
    Implementation of the colored thermostat for quantum nuclear effects
 ------------------------------------------------------------------------- */
 
+#include "fix_qtb.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
 #include <cstdlib>
-#include "fix_qtb.h"
-#include "math_extra.h"
 #include "atom.h"
-#include "atom_vec_ellipsoid.h"
 #include "force.h"
 #include "update.h"
 #include "modify.h"
 #include "compute.h"
-#include "domain.h"
-#include "region.h"
 #include "respa.h"
 #include "comm.h"
-#include "input.h"
-#include "variable.h"
 #include "random_mars.h"
 #include "memory.h"
 #include "error.h"
-#include "group.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-REAXC/compute_spec_atom.cpp b/src/USER-REAXC/compute_spec_atom.cpp
index 77b82b3e55..bc5b26b699 100644
--- a/src/USER-REAXC/compute_spec_atom.cpp
+++ b/src/USER-REAXC/compute_spec_atom.cpp
@@ -11,19 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
 #include "compute_spec_atom.h"
-#include "math_extra.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
-#include "domain.h"
 #include "memory.h"
 #include "error.h"
-
-#include "reaxc_defs.h"
-#include "reaxc_types.h"
 #include "pair_reaxc.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-REAXC/compute_spec_atom.h b/src/USER-REAXC/compute_spec_atom.h
index 4d5cb86d71..cf0aa0215d 100644
--- a/src/USER-REAXC/compute_spec_atom.h
+++ b/src/USER-REAXC/compute_spec_atom.h
@@ -21,7 +21,6 @@ ComputeStyle(SPEC/ATOM,ComputeSpecAtom)
 #define LMP_COMPUTE_SPEC_ATOM_H
 
 #include "compute.h"
-#include "pointers.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp
index 6c0da278c2..924b6806de 100644
--- a/src/USER-REAXC/fix_qeq_reax.cpp
+++ b/src/USER-REAXC/fix_qeq_reax.cpp
@@ -18,15 +18,13 @@
      Hybrid and sub-group capabilities: Ray Shan (Sandia)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "fix_qeq_reax.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "pair_reaxc.h"
 #include "atom.h"
 #include "comm.h"
-#include "domain.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
@@ -39,6 +37,7 @@
 #include "citeme.h"
 #include "error.h"
 #include "reaxc_defs.h"
+#include "reaxc_types.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-REAXC/fix_reaxc.cpp b/src/USER-REAXC/fix_reaxc.cpp
index dc67ad6ffb..c98adf5b45 100644
--- a/src/USER-REAXC/fix_reaxc.cpp
+++ b/src/USER-REAXC/fix_reaxc.cpp
@@ -23,8 +23,6 @@
 
 #include "fix_reaxc.h"
 #include "atom.h"
-#include "pair.h"
-#include "comm.h"
 #include "memory.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp
index 9dc347826f..f7ad7ed6d4 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.cpp
+++ b/src/USER-REAXC/fix_reaxc_bonds.cpp
@@ -15,22 +15,14 @@
    Contributing author: Ray Shan (Sandia, tnshan@sandia.gov)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
-#include "fix_ave_atom.h"
 #include "fix_reaxc_bonds.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "pair_reaxc.h"
-#include "modify.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "comm.h"
 #include "force.h"
-#include "compute.h"
-#include "input.h"
-#include "variable.h"
 #include "memory.h"
 #include "error.h"
 #include "reaxc_list.h"
diff --git a/src/USER-REAXC/fix_reaxc_bonds.h b/src/USER-REAXC/fix_reaxc_bonds.h
index d72f5446b5..e83e01f1d5 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.h
+++ b/src/USER-REAXC/fix_reaxc_bonds.h
@@ -20,9 +20,7 @@ FixStyle(reax/c/bonds,FixReaxCBonds)
 #ifndef LMP_FIX_REAXC_BONDS_H
 #define LMP_FIX_REAXC_BONDS_H
 
-#include <cstdio>
 #include "fix.h"
-#include "pointers.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp
index 46426d484a..74692f1c9b 100644
--- a/src/USER-REAXC/fix_reaxc_species.cpp
+++ b/src/USER-REAXC/fix_reaxc_species.cpp
@@ -16,27 +16,23 @@
                          Oleg Sergeev (VNIIA, sergeev@vniia.ru)
 ------------------------------------------------------------------------- */
 
+#include "fix_reaxc_species.h"
+#include <mpi.h>
 #include <cstdlib>
-#include <cmath>
 #include <cstring>
 #include "fix_ave_atom.h"
-#include "fix_reaxc_species.h"
 #include "atom.h"
 #include "domain.h"
 #include "update.h"
-#include "pair_reaxc.h"
 #include "modify.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "comm.h"
 #include "force.h"
-#include "compute.h"
-#include "input.h"
-#include "variable.h"
 #include "memory.h"
 #include "error.h"
-#include "reaxc_list.h"
+#include "pair_reaxc.h"
+#include "reaxc_defs.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-REAXC/fix_reaxc_species.h b/src/USER-REAXC/fix_reaxc_species.h
index 23a470fd0a..937af98527 100644
--- a/src/USER-REAXC/fix_reaxc_species.h
+++ b/src/USER-REAXC/fix_reaxc_species.h
@@ -21,11 +21,6 @@ FixStyle(reax/c/species,FixReaxCSpecies)
 #define LMP_FIX_REAXC_SPECIES_H
 
 #include "fix.h"
-#include "pointers.h"
-
-#include "pair_reaxc.h"
-#include "reaxc_types.h"
-#include "reaxc_defs.h"
 
 #define BUFLEN 1000
 
diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp
index 8f8dcfb8fc..959405576e 100644
--- a/src/USER-REAXC/pair_reaxc.cpp
+++ b/src/USER-REAXC/pair_reaxc.cpp
@@ -21,6 +21,11 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_reaxc.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include <strings.h>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
@@ -35,6 +40,7 @@
 #include "memory.h"
 #include "error.h"
 
+#include "reaxc_defs.h"
 #include "reaxc_types.h"
 #include "reaxc_allocate.h"
 #include "reaxc_control.h"
@@ -45,9 +51,7 @@
 #include "reaxc_list.h"
 #include "reaxc_lookup.h"
 #include "reaxc_reset_tools.h"
-#include "reaxc_traj.h"
 #include "reaxc_vector.h"
-#include "fix_reaxc_bonds.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp
index 460f8aeb6a..6303db5619 100644
--- a/src/USER-REAXC/reaxc_allocate.cpp
+++ b/src/USER-REAXC/reaxc_allocate.cpp
@@ -24,14 +24,13 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_allocate.h"
+#include <cstdlib>
+#include "reaxc_defs.h"
 #include "reaxc_list.h"
-#include "reaxc_reset_tools.h"
 #include "reaxc_tool_box.h"
-#include "reaxc_vector.h"
 
-#if defined(_OPENMP)
+#if defined(LMP_USER_OMP) && defined(_OPENMP)
 #include <omp.h>
 #endif
 
diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp
index 1ed58a0bfd..869e796661 100644
--- a/src/USER-REAXC/reaxc_bond_orders.cpp
+++ b/src/USER-REAXC/reaxc_bond_orders.cpp
@@ -24,9 +24,11 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
-#include "reaxc_types.h"
 #include "reaxc_bond_orders.h"
+#include <cmath>
+#include "pair.h"
+#include "reaxc_defs.h"
+#include "reaxc_types.h"
 #include "reaxc_list.h"
 #include "reaxc_vector.h"
 
diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp
index 48fb872324..4cfd2a3c3a 100644
--- a/src/USER-REAXC/reaxc_bonds.cpp
+++ b/src/USER-REAXC/reaxc_bonds.cpp
@@ -24,12 +24,11 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_bonds.h"
-#include "reaxc_bond_orders.h"
+#include <cmath>
+#include "pair.h"
+#include "reaxc_defs.h"
 #include "reaxc_list.h"
-#include "reaxc_tool_box.h"
-#include "reaxc_vector.h"
 
 void Bonds( reax_system *system, control_params * /*control*/,
             simulation_data *data, storage *workspace, reax_list **lists,
diff --git a/src/USER-REAXC/reaxc_control.cpp b/src/USER-REAXC/reaxc_control.cpp
index 535226fff8..12aa989fa2 100644
--- a/src/USER-REAXC/reaxc_control.cpp
+++ b/src/USER-REAXC/reaxc_control.cpp
@@ -24,8 +24,10 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_control.h"
+#include <cstdlib>
+#include <cstring>
+#include "reaxc_defs.h"
 #include "reaxc_tool_box.h"
 
 #include "error.h"
diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp
index 9534637645..e3a6645fc2 100644
--- a/src/USER-REAXC/reaxc_ffield.cpp
+++ b/src/USER-REAXC/reaxc_ffield.cpp
@@ -24,12 +24,16 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
-#include "error.h"
 #include "reaxc_ffield.h"
+#include <mpi.h>
+#include <cctype>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include "reaxc_defs.h"
+#include "error.h"
 #include "reaxc_tool_box.h"
 
-
 char Read_Force_Field( FILE *fp, reax_interaction *reax,
                        control_params *control )
 {
diff --git a/src/USER-REAXC/reaxc_ffield.h b/src/USER-REAXC/reaxc_ffield.h
index 7cef730f91..b6fe1c9ea9 100644
--- a/src/USER-REAXC/reaxc_ffield.h
+++ b/src/USER-REAXC/reaxc_ffield.h
@@ -28,6 +28,7 @@
 #define __FFIELD_H_
 
 #include "reaxc_types.h"
+#include <cstdio>
 
 char Read_Force_Field( FILE*, reax_interaction*, control_params* );
 
diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp
index 186cde681a..6cd627f05d 100644
--- a/src/USER-REAXC/reaxc_forces.cpp
+++ b/src/USER-REAXC/reaxc_forces.cpp
@@ -24,24 +24,22 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_forces.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "reaxc_bond_orders.h"
 #include "reaxc_bonds.h"
 #include "reaxc_hydrogen_bonds.h"
-#include "reaxc_io_tools.h"
 #include "reaxc_list.h"
-#include "reaxc_lookup.h"
 #include "reaxc_multi_body.h"
 #include "reaxc_nonbonded.h"
-#include "reaxc_tool_box.h"
 #include "reaxc_torsion_angles.h"
 #include "reaxc_valence_angles.h"
 #include "reaxc_vector.h"
 
 #include "error.h"
 
-
 interaction_function Interaction_Functions[NUM_INTRS];
 
 void Dummy_Interaction( reax_system * /*system*/, control_params * /*control*/,
diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
index be34df7571..5929703bad 100644
--- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
+++ b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
@@ -24,9 +24,10 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_hydrogen_bonds.h"
-#include "reaxc_bond_orders.h"
+#include <cmath>
+#include "pair.h"
+#include "reaxc_defs.h"
 #include "reaxc_list.h"
 #include "reaxc_valence_angles.h"
 #include "reaxc_vector.h"
diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp
index df5de49034..966ad78c34 100644
--- a/src/USER-REAXC/reaxc_init_md.cpp
+++ b/src/USER-REAXC/reaxc_init_md.cpp
@@ -24,17 +24,19 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_init_md.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include "reaxc_defs.h"
 #include "reaxc_allocate.h"
 #include "reaxc_forces.h"
 #include "reaxc_io_tools.h"
 #include "reaxc_list.h"
 #include "reaxc_lookup.h"
 #include "reaxc_reset_tools.h"
-#include "reaxc_system_props.h"
 #include "reaxc_tool_box.h"
-#include "reaxc_vector.h"
 
 #include "error.h"
 
diff --git a/src/USER-REAXC/reaxc_init_md.h b/src/USER-REAXC/reaxc_init_md.h
index ab519a4c72..5d593f50ea 100644
--- a/src/USER-REAXC/reaxc_init_md.h
+++ b/src/USER-REAXC/reaxc_init_md.h
@@ -28,7 +28,7 @@
 #define __INIT_MD_H_
 
 #include "reaxc_types.h"
-
+#include <mpi.h>
 
 void Initialize( reax_system*, control_params*, simulation_data*, storage*,
                  reax_list**, output_controls*, mpi_datatypes*, MPI_Comm );
diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp
index 51aa8bca0f..f68a2a2abb 100644
--- a/src/USER-REAXC/reaxc_io_tools.cpp
+++ b/src/USER-REAXC/reaxc_io_tools.cpp
@@ -24,15 +24,12 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
-#include "update.h"
 #include "reaxc_io_tools.h"
-#include "reaxc_list.h"
-#include "reaxc_reset_tools.h"
+#include <cstdio>
+#include <cstring>
+#include "reaxc_defs.h"
 #include "reaxc_system_props.h"
-#include "reaxc_tool_box.h"
 #include "reaxc_traj.h"
-#include "reaxc_vector.h"
 
 int Init_Output_Files( reax_system *system, control_params *control,
                        output_controls *out_control, mpi_datatypes *mpi_data,
@@ -85,7 +82,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
 
 
 /************************ close output files ************************/
-int Close_Output_Files( reax_system *system, control_params *control,
+int Close_Output_Files( reax_system *system, control_params * /* control */,
                         output_controls *out_control, mpi_datatypes * /*mpi_data*/ )
 {
   if (out_control->write_steps > 0)
diff --git a/src/USER-REAXC/reaxc_list.cpp b/src/USER-REAXC/reaxc_list.cpp
index cd4f815286..53bd05bc8d 100644
--- a/src/USER-REAXC/reaxc_list.cpp
+++ b/src/USER-REAXC/reaxc_list.cpp
@@ -24,8 +24,8 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_list.h"
+#include "reaxc_defs.h"
 #include "reaxc_tool_box.h"
 
 #include "error.h"
diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp
index 8d33a33fba..622483fdc9 100644
--- a/src/USER-REAXC/reaxc_lookup.cpp
+++ b/src/USER-REAXC/reaxc_lookup.cpp
@@ -24,12 +24,13 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_lookup.h"
+#include <mpi.h>
+#include <cstdlib>
+#include "reaxc_defs.h"
 #include "reaxc_nonbonded.h"
 #include "reaxc_tool_box.h"
 
-
 void Tridiagonal_Solve( const double *a, const double *b,
                         double *c, double *d, double *x, unsigned int n){
   int i;
diff --git a/src/USER-REAXC/reaxc_lookup.h b/src/USER-REAXC/reaxc_lookup.h
index 3fd0c2581a..3aae7e0b63 100644
--- a/src/USER-REAXC/reaxc_lookup.h
+++ b/src/USER-REAXC/reaxc_lookup.h
@@ -28,6 +28,7 @@
 #define __LOOKUP_H_
 
 #include "reaxc_types.h"
+namespace LAMMPS_NS { class Error; }
 
 void Tridiagonal_Solve( const double *a, const double *b,
                         double *c, double *d, double *x, unsigned int n);
@@ -35,8 +36,9 @@ void Tridiagonal_Solve( const double *a, const double *b,
 void Natural_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f,
                            cubic_spline_coef *coef, unsigned int n );
 
-void Complete_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, double v0, double vlast,
-                            cubic_spline_coef *coef, unsigned int n );
+void Complete_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f,
+                            double v0, double vlast, cubic_spline_coef *coef,
+                            unsigned int n );
 
 int Init_Lookup_Tables( reax_system*, control_params*, storage*,
                         mpi_datatypes*, char* );
diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp
index f7d72a2678..ed1a3d5ac1 100644
--- a/src/USER-REAXC/reaxc_multi_body.cpp
+++ b/src/USER-REAXC/reaxc_multi_body.cpp
@@ -24,11 +24,12 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_multi_body.h"
-#include "reaxc_bond_orders.h"
+#include <cmath>
+#include <cstring>
+#include "pair.h"
+#include "reaxc_defs.h"
 #include "reaxc_list.h"
-#include "reaxc_vector.h"
 
 void Atom_Energy( reax_system *system, control_params *control,
                   simulation_data *data, storage *workspace, reax_list **lists,
diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp
index b0fea8c1b9..497a1a0ebe 100644
--- a/src/USER-REAXC/reaxc_nonbonded.cpp
+++ b/src/USER-REAXC/reaxc_nonbonded.cpp
@@ -24,10 +24,11 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
-#include "reaxc_types.h"
 #include "reaxc_nonbonded.h"
-#include "reaxc_bond_orders.h"
+#include <cmath>
+#include "pair.h"
+#include "reaxc_defs.h"
+#include "reaxc_types.h"
 #include "reaxc_list.h"
 #include "reaxc_vector.h"
 
diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp
index e00656694c..91b1a9e14f 100644
--- a/src/USER-REAXC/reaxc_reset_tools.cpp
+++ b/src/USER-REAXC/reaxc_reset_tools.cpp
@@ -24,8 +24,9 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_reset_tools.h"
+#include <cstring>
+#include "reaxc_defs.h"
 #include "reaxc_list.h"
 #include "reaxc_tool_box.h"
 #include "reaxc_vector.h"
diff --git a/src/USER-REAXC/reaxc_system_props.cpp b/src/USER-REAXC/reaxc_system_props.cpp
index 5024feffcf..166f070be6 100644
--- a/src/USER-REAXC/reaxc_system_props.cpp
+++ b/src/USER-REAXC/reaxc_system_props.cpp
@@ -24,11 +24,9 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_system_props.h"
-#include "reaxc_tool_box.h"
-#include "reaxc_vector.h"
-
+#include <mpi.h>
+#include "reaxc_defs.h"
 
 void Compute_System_Energy( reax_system *system, simulation_data *data,
                             MPI_Comm comm )
diff --git a/src/USER-REAXC/reaxc_system_props.h b/src/USER-REAXC/reaxc_system_props.h
index 161060e184..4d80e22966 100644
--- a/src/USER-REAXC/reaxc_system_props.h
+++ b/src/USER-REAXC/reaxc_system_props.h
@@ -28,6 +28,7 @@
 #define __SYSTEM_PROP_H_
 
 #include "reaxc_types.h"
+#include <mpi.h>
 
 void Compute_System_Energy( reax_system*, simulation_data*, MPI_Comm );
 
diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp
index ffe42e37bb..811c2ed0ee 100644
--- a/src/USER-REAXC/reaxc_tool_box.cpp
+++ b/src/USER-REAXC/reaxc_tool_box.cpp
@@ -24,8 +24,15 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_tool_box.h"
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "reaxc_defs.h"
+
+#if !defined(_MSC_VER)
+#include <sys/time.h>
+#endif
 
 #include "error.h"
 
diff --git a/src/USER-REAXC/reaxc_tool_box.h b/src/USER-REAXC/reaxc_tool_box.h
index 0465376dba..b325819265 100644
--- a/src/USER-REAXC/reaxc_tool_box.h
+++ b/src/USER-REAXC/reaxc_tool_box.h
@@ -28,7 +28,7 @@
 #define __TOOL_BOX_H_
 
 #include "reaxc_types.h"
-#include "reaxc_defs.h"
+namespace LAMMPS_NS { class Error; }
 
 /* from system_props.h */
 double Get_Time( );
diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp
index ed76368d68..ce944b217f 100644
--- a/src/USER-REAXC/reaxc_torsion_angles.cpp
+++ b/src/USER-REAXC/reaxc_torsion_angles.cpp
@@ -24,11 +24,11 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_torsion_angles.h"
-#include "reaxc_bond_orders.h"
+#include <cmath>
+#include "pair.h"
+#include "reaxc_defs.h"
 #include "reaxc_list.h"
-#include "reaxc_tool_box.h"
 #include "reaxc_vector.h"
 
 #define MIN_SINE 1e-10
diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp
index 356d7b6eeb..fb493feae5 100644
--- a/src/USER-REAXC/reaxc_traj.cpp
+++ b/src/USER-REAXC/reaxc_traj.cpp
@@ -24,10 +24,13 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_traj.h"
+#include <mpi.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "reaxc_defs.h"
 #include "reaxc_list.h"
-#include "reaxc_tool_box.h"
 
 #include "error.h"
 
diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h
index 0821c065cc..319c373927 100644
--- a/src/USER-REAXC/reaxc_types.h
+++ b/src/USER-REAXC/reaxc_types.h
@@ -27,19 +27,11 @@
 #ifndef __REAX_TYPES_H_
 #define __REAX_TYPES_H_
 
-#include <mpi.h>
 #include "lmptype.h"
-
-#include <cctype>
-#include <cmath>
+#include <mpi.h>
 #include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <ctime>
-#include <sys/time.h>
 #include "accelerator_kokkos.h"
 
-
 namespace LAMMPS_NS { class Error;}
 
 #if defined LMP_USER_OMP
diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp
index 4ba870b6d9..560955fa9d 100644
--- a/src/USER-REAXC/reaxc_valence_angles.cpp
+++ b/src/USER-REAXC/reaxc_valence_angles.cpp
@@ -24,9 +24,10 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_valence_angles.h"
-#include "reaxc_bond_orders.h"
+#include <cmath>
+#include "pair.h"
+#include "reaxc_defs.h"
 #include "reaxc_list.h"
 #include "reaxc_vector.h"
 
diff --git a/src/USER-REAXC/reaxc_vector.cpp b/src/USER-REAXC/reaxc_vector.cpp
index b54d329ce9..207d745df3 100644
--- a/src/USER-REAXC/reaxc_vector.cpp
+++ b/src/USER-REAXC/reaxc_vector.cpp
@@ -24,9 +24,9 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reaxc.h"
 #include "reaxc_vector.h"
-
+#include <cmath>
+#include "reaxc_defs.h"
 
 void rvec_Copy( rvec dest, rvec src )
 {
diff --git a/src/USER-REAXC/reaxc_vector.h b/src/USER-REAXC/reaxc_vector.h
index 906b200dc9..549c1f927c 100644
--- a/src/USER-REAXC/reaxc_vector.h
+++ b/src/USER-REAXC/reaxc_vector.h
@@ -27,9 +27,7 @@
 #ifndef __VECTOR_H_
 #define __VECTOR_H_
 
-#include "pair.h"
 #include "reaxc_types.h"
-#include "reaxc_defs.h"
 
 void rvec_Copy( rvec, rvec );
 void rvec_Scale( rvec, double, rvec );
diff --git a/src/USER-SDPD/fix_meso_move.cpp b/src/USER-SDPD/fix_meso_move.cpp
index 85b08a2af7..176cd8b895 100644
--- a/src/USER-SDPD/fix_meso_move.cpp
+++ b/src/USER-SDPD/fix_meso_move.cpp
@@ -16,11 +16,10 @@
       Morteza Jalalvand (IASBS)  jalalvand.m AT gmail.com
 ------------------------------------------------------------------------- */
 
+#include "fix_meso_move.h"
 #include <cstring>
 #include <cmath>
-#include "fix_meso_move.h"
 #include "atom.h"
-#include "group.h"
 #include "update.h"
 #include "modify.h"
 #include "force.h"
diff --git a/src/USER-SDPD/fix_rigid_meso.cpp b/src/USER-SDPD/fix_rigid_meso.cpp
index 49c9ca8614..e93c543e72 100644
--- a/src/USER-SDPD/fix_rigid_meso.cpp
+++ b/src/USER-SDPD/fix_rigid_meso.cpp
@@ -27,17 +27,10 @@
     and all codes relevant to that has been removed
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "fix_rigid_meso.h"
 #include "math_extra.h"
 #include "atom.h"
-#include "compute.h"
 #include "domain.h"
-#include "update.h"
-#include "modify.h"
-#include "group.h"
-#include "force.h"
-#include "output.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp
index db80debe51..d799869db3 100644
--- a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp
+++ b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp
@@ -18,9 +18,8 @@
     references: Espanol and Revenga, Phys Rev E 67, 026705 (2003)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sdpd_taitwater_isothermal.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp
index 9c634be091..604504c5a7 100644
--- a/src/USER-SMD/atom_vec_smd.cpp
+++ b/src/USER-SMD/atom_vec_smd.cpp
@@ -22,24 +22,19 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "atom_vec_smd.h"
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
 #include "modify.h"
-#include "force.h"
 #include "fix.h"
-#include "fix_adapt.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "utils.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
+
 #define NMAT_FULL 9
 #define NMAT_SYMM 6
 
diff --git a/src/USER-SMD/compute_smd_contact_radius.cpp b/src/USER-SMD/compute_smd_contact_radius.cpp
index 8193ad6ccf..46cbc602f2 100644
--- a/src/USER-SMD/compute_smd_contact_radius.cpp
+++ b/src/USER-SMD/compute_smd_contact_radius.cpp
@@ -23,13 +23,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_smd_contact_radius.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-SMD/compute_smd_damage.cpp b/src/USER-SMD/compute_smd_damage.cpp
index 9603fd5c64..96a936cd82 100644
--- a/src/USER-SMD/compute_smd_damage.cpp
+++ b/src/USER-SMD/compute_smd_damage.cpp
@@ -23,13 +23,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_smd_damage.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-SMD/compute_smd_internal_energy.cpp b/src/USER-SMD/compute_smd_internal_energy.cpp
index d937aa98a4..f88da8bc33 100644
--- a/src/USER-SMD/compute_smd_internal_energy.cpp
+++ b/src/USER-SMD/compute_smd_internal_energy.cpp
@@ -29,7 +29,6 @@
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-SMD/compute_smd_plastic_strain.cpp b/src/USER-SMD/compute_smd_plastic_strain.cpp
index 67466ebb72..c1c001a5dd 100644
--- a/src/USER-SMD/compute_smd_plastic_strain.cpp
+++ b/src/USER-SMD/compute_smd_plastic_strain.cpp
@@ -23,13 +23,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_smd_plastic_strain.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp
index 20dfa64edd..272a2c59e5 100644
--- a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp
+++ b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp
@@ -23,13 +23,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_smd_plastic_strain_rate.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-SMD/compute_smd_rho.cpp b/src/USER-SMD/compute_smd_rho.cpp
index 5c78e604b6..d9c0a99b07 100644
--- a/src/USER-SMD/compute_smd_rho.cpp
+++ b/src/USER-SMD/compute_smd_rho.cpp
@@ -22,13 +22,12 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_smd_rho.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
index 37ad78dcea..09aeeea74a 100644
--- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
@@ -22,20 +22,16 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <Eigen/Eigen>
 #include "compute_smd_tlsph_defgrad.h"
+#include <cstring>
+#include <Eigen/Eigen>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
-#include "pair.h"
+
 using namespace Eigen;
 using namespace std;
 using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp
index bbab274b5c..ba1a9306ef 100644
--- a/src/USER-SMD/compute_smd_tlsph_shape.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp
@@ -22,13 +22,9 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <Eigen/Eigen>
-#include <Eigen/Geometry>
 #include "compute_smd_tlsph_shape.h"
+#include <cstring>
+#include <Eigen/Eigen>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp
index a94a3cd511..f0061bf7a1 100644
--- a/src/USER-SMD/compute_smd_tlsph_strain.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp
@@ -23,12 +23,9 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <Eigen/Eigen>
 #include "compute_smd_tlsph_strain.h"
+#include <cstring>
+#include <Eigen/Eigen>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/USER-SMD/compute_smd_tlsph_stress.cpp b/src/USER-SMD/compute_smd_tlsph_stress.cpp
index a54b07dd1e..9c78b192ce 100644
--- a/src/USER-SMD/compute_smd_tlsph_stress.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_stress.cpp
@@ -22,9 +22,10 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
+#include "compute_smd_tlsph_stress.h"
+#include <cmath>
 #include <cstring>
 #include <Eigen/Eigen>
-#include "compute_smd_tlsph_stress.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/USER-SMD/compute_smd_triangle_vertices.cpp b/src/USER-SMD/compute_smd_triangle_vertices.cpp
index b24223b8b5..06706a85ad 100644
--- a/src/USER-SMD/compute_smd_triangle_vertices.cpp
+++ b/src/USER-SMD/compute_smd_triangle_vertices.cpp
@@ -23,22 +23,15 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <Eigen/Eigen>
 #include "compute_smd_triangle_vertices.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
-#include "pair.h"
 
-using namespace Eigen;
 using namespace std;
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-SMD/compute_smd_ulsph_strain.cpp b/src/USER-SMD/compute_smd_ulsph_strain.cpp
index 89b85f7bc1..cf1535759c 100644
--- a/src/USER-SMD/compute_smd_ulsph_strain.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_strain.cpp
@@ -23,22 +23,15 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <Eigen/Eigen>
 #include "compute_smd_ulsph_strain.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
-#include "pair.h"
 
-using namespace Eigen;
 using namespace std;
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-SMD/compute_smd_ulsph_stress.cpp b/src/USER-SMD/compute_smd_ulsph_stress.cpp
index 7f1bbc4c29..ea477375ce 100644
--- a/src/USER-SMD/compute_smd_ulsph_stress.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_stress.cpp
@@ -22,9 +22,10 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
+#include "compute_smd_ulsph_stress.h"
+#include <cmath>
 #include <cstring>
 #include <Eigen/Eigen>
-#include "compute_smd_ulsph_stress.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp
index 17a6b556e8..eb1f144275 100644
--- a/src/USER-SMD/compute_smd_vol.cpp
+++ b/src/USER-SMD/compute_smd_vol.cpp
@@ -22,13 +22,13 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_smd_vol.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp
index f015c6c4df..ab6dd5ef5c 100644
--- a/src/USER-SMD/fix_smd_adjust_dt.cpp
+++ b/src/USER-SMD/fix_smd_adjust_dt.cpp
@@ -22,21 +22,14 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_smd_adjust_dt.h"
-#include "atom.h"
+#include <mpi.h>
+#include <cstdlib>
 #include "update.h"
-#include "integrate.h"
-#include "domain.h"
-#include "lattice.h"
 #include "force.h"
 #include "pair.h"
 #include "modify.h"
 #include "fix.h"
-#include "output.h"
-#include "dump.h"
 #include "comm.h"
 #include "error.h"
 
diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
index f931ae94ff..8464bed609 100644
--- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
@@ -22,22 +22,16 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <Eigen/Eigen>
 #include "fix_smd_integrate_tlsph.h"
+#include <cmath>
+#include <cstring>
+#include <Eigen/Eigen>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "error.h"
 #include "pair.h"
-#include "neigh_list.h"
-#include "domain.h"
-#include "neighbor.h"
 #include "comm.h"
-#include "modify.h"
 
 using namespace Eigen;
 using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
index 6c4705eb96..0f0d224f95 100644
--- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
@@ -22,25 +22,16 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
+#include "fix_smd_integrate_ulsph.h"
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
 #include <Eigen/Eigen>
-#include "fix_smd_integrate_ulsph.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
-#include "respa.h"
-#include "memory.h"
 #include "error.h"
 #include "pair.h"
-#include "domain.h"
 
 using namespace Eigen;
 using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
index fe8695b23e..cbaad9ac4c 100644
--- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
+++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
@@ -22,25 +22,15 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
-#include <cmath>
-#include <cstdlib>
-#include <Eigen/Eigen>
 #include "fix_smd_move_triangulated_surface.h"
+#include <cmath>
+#include <cstring>
+#include <Eigen/Eigen>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
-#include "respa.h"
-#include "memory.h"
 #include "error.h"
-#include "pair.h"
-#include "domain.h"
 #include "math_const.h"
 
 using namespace Eigen;
diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp
index 4bc8b5127b..2964ded544 100644
--- a/src/USER-SMD/fix_smd_setvel.cpp
+++ b/src/USER-SMD/fix_smd_setvel.cpp
@@ -23,9 +23,9 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "fix_smd_setvel.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
index a2813cc3ca..6aa23fe3b2 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
@@ -24,20 +24,16 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
-#include <cstdio>
-#include <Eigen/Eigen>
 #include "fix_smd_tlsph_reference_configuration.h"
+#include <mpi.h>
+#include <Eigen/Eigen>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "lattice.h"
 #include "force.h"
 #include "pair.h"
 #include "update.h"
-#include "modify.h"
 #include "memory.h"
 #include "error.h"
 #include "domain.h"
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h
index 8549621c2f..5f952bde93 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h
@@ -35,7 +35,6 @@ FixStyle(SMD_TLSPH_NEIGHBORS,FixSMD_TLSPH_ReferenceConfiguration)
 #define LMP_FIX_SMD_TLSPH_REFERENCE_H
 
 #include "fix.h"
-#include "my_page.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp
index a37ba67a80..9183bcd9ea 100644
--- a/src/USER-SMD/fix_smd_wall_surface.cpp
+++ b/src/USER-SMD/fix_smd_wall_surface.cpp
@@ -15,21 +15,15 @@
    Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
-#include <cstdio>
-#include <Eigen/Eigen>
 #include "fix_smd_wall_surface.h"
+#include <mpi.h>
+#include <cstring>
+#include <cstdlib>
+#include <Eigen/Eigen>
 #include "atom.h"
 #include "domain.h"
 #include "force.h"
 #include "comm.h"
-#include "update.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "pair.h"
-#include "lattice.h"
 #include "memory.h"
 #include "error.h"
 #include "atom_vec.h"
diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp
index 541be9f05c..97be94d833 100644
--- a/src/USER-SMD/pair_smd_hertz.cpp
+++ b/src/USER-SMD/pair_smd_hertz.cpp
@@ -26,17 +26,14 @@
    Contributing author: Mike Parks (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_smd_hertz.h"
+#include <mpi.h>
 #include <cmath>
-#include <cfloat>
 #include <cstdlib>
 #include <cstring>
-#include "pair_smd_hertz.h"
 #include "atom.h"
 #include "domain.h"
 #include "force.h"
-#include "update.h"
-#include "modify.h"
-#include "fix.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp
index 1d7bbca780..82b7c8ff9d 100644
--- a/src/USER-SMD/pair_smd_tlsph.cpp
+++ b/src/USER-SMD/pair_smd_tlsph.cpp
@@ -22,15 +22,13 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cfloat>
-#include <cstdlib>
-#include <cstring>
-#include <cstdio>
-#include <iostream>
-#include <map>
-#include <Eigen/Eigen>
 #include "pair_smd_tlsph.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <string>
+#include <iostream>
+#include <Eigen/Eigen>
 #include "fix_smd_tlsph_reference_configuration.h"
 #include "atom.h"
 #include "domain.h"
@@ -41,12 +39,9 @@
 #include "fix.h"
 #include "comm.h"
 #include "neighbor.h"
-#include "neigh_list.h"
 #include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
-#include "math_special.h"
-#include "update.h"
 #include "smd_material_models.h"
 #include "smd_kernels.h"
 #include "smd_math.h"
@@ -1781,9 +1776,8 @@ void PairTlsph::init_style() {
  optional granular history list
  ------------------------------------------------------------------------- */
 
-void PairTlsph::init_list(int id, NeighList *ptr) {
-        if (id == 0)
-                list = ptr;
+void PairTlsph::init_list(int id, class NeighList *ptr) {
+  if (id == 0) list = ptr;
 }
 
 /* ----------------------------------------------------------------------
@@ -1791,8 +1785,7 @@ void PairTlsph::init_list(int id, NeighList *ptr) {
  ------------------------------------------------------------------------- */
 
 double PairTlsph::memory_usage() {
-
-        return 118 * nmax * sizeof(double);
+  return 118.0 * nmax * sizeof(double);
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp
index d3a4983379..f9052be087 100644
--- a/src/USER-SMD/pair_smd_triangulated_surface.cpp
+++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp
@@ -26,20 +26,15 @@
    Contributing author: Mike Parks (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_smd_triangulated_surface.h"
+#include <mpi.h>
 #include <cmath>
-#include <cfloat>
 #include <cstdlib>
 #include <cstring>
-#include <cstdio>
-#include <iostream>
 #include <Eigen/Eigen>
-#include "pair_smd_triangulated_surface.h"
 #include "atom.h"
 #include "domain.h"
 #include "force.h"
-#include "update.h"
-#include "modify.h"
-#include "fix.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp
index 2c4a2de989..b53eb779de 100644
--- a/src/USER-SMD/pair_smd_ulsph.cpp
+++ b/src/USER-SMD/pair_smd_ulsph.cpp
@@ -22,19 +22,16 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cfloat>
-#include <cstdlib>
-#include <cstring>
-#include <cstdio>
-#include <iostream>
 #include "pair_smd_ulsph.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <string>
+#include <utility>
 #include "atom.h"
 #include "domain.h"
 #include "force.h"
 #include "update.h"
-#include "modify.h"
-#include "fix.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp
index 4213428872..5ee67fbb4e 100644
--- a/src/USER-SMD/smd_material_models.cpp
+++ b/src/USER-SMD/smd_material_models.cpp
@@ -21,6 +21,10 @@
 
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
+#include "smd_material_models.h"
+#include <cmath>
+#include <cstdlib>
+#include <utility>
 #include <iostream>
 #include <cstdio>
 #include "math_special.h"
diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp
index ba7f8eb88c..f61fc1a72e 100644
--- a/src/USER-SMTBQ/pair_smtbq.cpp
+++ b/src/USER-SMTBQ/pair_smtbq.cpp
@@ -38,25 +38,24 @@
    <http://www.gnu.org/licenses/>.
    ------------------------------------------------------------------------- */
 
+#include "pair_smtbq.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
+#include <algorithm>
 #include <vector>
-#include "pair_smtbq.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "group.h"
 #include "update.h"
 #include "math_const.h"
 #include "math_special.h"
 #include "memory.h"
 #include "error.h"
-#include "domain.h"
 
 #include <fstream>
 #include <iomanip>
diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp
index aa3e680c61..cd7c2251ab 100644
--- a/src/USER-SPH/atom_vec_meso.cpp
+++ b/src/USER-SPH/atom_vec_meso.cpp
@@ -11,13 +11,11 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "atom_vec_meso.h"
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "memory.h"
diff --git a/src/USER-SPH/compute_meso_e_atom.cpp b/src/USER-SPH/compute_meso_e_atom.cpp
index e39dee2b5f..c56243e5ed 100644
--- a/src/USER-SPH/compute_meso_e_atom.cpp
+++ b/src/USER-SPH/compute_meso_e_atom.cpp
@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_meso_e_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-SPH/compute_meso_rho_atom.cpp b/src/USER-SPH/compute_meso_rho_atom.cpp
index eeb3f987bc..b2fbd2d70a 100644
--- a/src/USER-SPH/compute_meso_rho_atom.cpp
+++ b/src/USER-SPH/compute_meso_rho_atom.cpp
@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_meso_rho_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-SPH/compute_meso_t_atom.cpp b/src/USER-SPH/compute_meso_t_atom.cpp
index dc4f3407f1..bab96468dd 100644
--- a/src/USER-SPH/compute_meso_t_atom.cpp
+++ b/src/USER-SPH/compute_meso_t_atom.cpp
@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_meso_t_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-SPH/fix_meso.cpp b/src/USER-SPH/fix_meso.cpp
index b688eccfea..4f4e532291 100644
--- a/src/USER-SPH/fix_meso.cpp
+++ b/src/USER-SPH/fix_meso.cpp
@@ -11,23 +11,11 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
-#include <cmath>
-#include <cstdlib>
 #include "fix_meso.h"
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
-#include "respa.h"
-#include "memory.h"
 #include "error.h"
-#include "pair.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp
index 29e8a1554c..b7f0675ef8 100644
--- a/src/USER-SPH/fix_meso_stationary.cpp
+++ b/src/USER-SPH/fix_meso_stationary.cpp
@@ -11,23 +11,11 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
-#include <cmath>
-#include <cstdlib>
 #include "fix_meso_stationary.h"
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
-#include "respa.h"
-#include "memory.h"
 #include "error.h"
-#include "pair.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp
index bafa26be89..cff9009015 100644
--- a/src/USER-SPH/pair_sph_heatconduction.cpp
+++ b/src/USER-SPH/pair_sph_heatconduction.cpp
@@ -11,12 +11,10 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sph_heatconduction.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
-#include "comm.h"
 #include "memory.h"
 #include "error.h"
 #include "neigh_list.h"
diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp
index db5ec964bc..f206bf68f5 100644
--- a/src/USER-SPH/pair_sph_idealgas.cpp
+++ b/src/USER-SPH/pair_sph_idealgas.cpp
@@ -11,12 +11,10 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sph_idealgas.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
-#include "comm.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp
index 7d315c975c..3173e2a47d 100644
--- a/src/USER-SPH/pair_sph_lj.cpp
+++ b/src/USER-SPH/pair_sph_lj.cpp
@@ -11,12 +11,10 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sph_lj.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
-#include "comm.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp
index 842dddc744..fa51dc3781 100644
--- a/src/USER-SPH/pair_sph_rhosum.cpp
+++ b/src/USER-SPH/pair_sph_rhosum.cpp
@@ -11,8 +11,6 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sph_rhosum.h"
 #include "atom.h"
 #include "force.h"
diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp
index cf3c0e914b..f2a34d4edd 100644
--- a/src/USER-SPH/pair_sph_taitwater.cpp
+++ b/src/USER-SPH/pair_sph_taitwater.cpp
@@ -11,9 +11,8 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sph_taitwater.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp
index 5cbaa5959f..9ca03e3476 100644
--- a/src/USER-SPH/pair_sph_taitwater_morris.cpp
+++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp
@@ -11,9 +11,8 @@
  See the README file in the top-level LAMMPS directory.
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_sph_taitwater_morris.h"
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp
index 3339e0555b..9d15fbc441 100644
--- a/src/USER-TALLY/compute_force_tally.cpp
+++ b/src/USER-TALLY/compute_force_tally.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cmath>
 #include "compute_force_tally.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "group.h"
 #include "pair.h"
diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp
index 2a5f724953..350bc4b4b6 100644
--- a/src/USER-TALLY/compute_heat_flux_tally.cpp
+++ b/src/USER-TALLY/compute_heat_flux_tally.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_heat_flux_tally.h"
+#include <mpi.h>
 #include "atom.h"
 #include "group.h"
 #include "pair.h"
diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/USER-TALLY/compute_pe_mol_tally.cpp
index 5fabd4a77b..ce647a04c3 100644
--- a/src/USER-TALLY/compute_pe_mol_tally.cpp
+++ b/src/USER-TALLY/compute_pe_mol_tally.cpp
@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_pe_mol_tally.h"
+#include <mpi.h>
 #include "atom.h"
 #include "group.h"
 #include "pair.h"
 #include "update.h"
-#include "memory.h"
 #include "error.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp
index 8e6703bde1..edfa49b1b1 100644
--- a/src/USER-TALLY/compute_pe_tally.cpp
+++ b/src/USER-TALLY/compute_pe_tally.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_pe_tally.h"
+#include <mpi.h>
 #include "atom.h"
 #include "group.h"
 #include "pair.h"
diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp
index 07d685a9c2..1ea096e286 100644
--- a/src/USER-TALLY/compute_stress_tally.cpp
+++ b/src/USER-TALLY/compute_stress_tally.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_stress_tally.h"
+#include <mpi.h>
 #include "atom.h"
 #include "group.h"
 #include "pair.h"
diff --git a/src/USER-UEF/compute_pressure_uef.cpp b/src/USER-UEF/compute_pressure_uef.cpp
index 8b62853042..adb9970c12 100644
--- a/src/USER-UEF/compute_pressure_uef.cpp
+++ b/src/USER-UEF/compute_pressure_uef.cpp
@@ -13,21 +13,14 @@
    Contributing author: David Nicholson (MIT)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
-#include <cstdlib>
 #include "compute_pressure_uef.h"
+#include <cstring>
 #include "fix_nh_uef.h"
 #include "update.h"
 #include "domain.h"
 #include "modify.h"
 #include "fix.h"
 #include "force.h"
-#include "pair.h"
-#include "bond.h"
-#include "angle.h"
-#include "dihedral.h"
-#include "improper.h"
 #include "kspace.h"
 #include "error.h"
 
diff --git a/src/USER-UEF/compute_temp_uef.cpp b/src/USER-UEF/compute_temp_uef.cpp
index 999296ec7e..698c4452c2 100644
--- a/src/USER-UEF/compute_temp_uef.cpp
+++ b/src/USER-UEF/compute_temp_uef.cpp
@@ -13,11 +13,9 @@
    Contributing author: David Nicholson (MIT)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "compute_temp_uef.h"
+#include <cstring>
 #include "fix_nh_uef.h"
-#include "update.h"
 #include "modify.h"
 #include "fix.h"
 #include "error.h"
diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/USER-UEF/dump_cfg_uef.cpp
index 58b3ec5a1f..8e6268eee6 100644
--- a/src/USER-UEF/dump_cfg_uef.cpp
+++ b/src/USER-UEF/dump_cfg_uef.cpp
@@ -13,15 +13,10 @@
    Contributing Author: David Nicholson (MIT)
 ------------------------------------------------------------------------- */
 
-
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "dump_cfg.h"
+#include <cstring>
 #include "atom.h"
-#include "domain.h"
 #include "modify.h"
-#include "compute.h"
 #include "fix.h"
 #include "error.h"
 #include "uef_utils.h"
diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp
index bffcd7849f..8873688eb7 100644
--- a/src/USER-UEF/fix_nh_uef.cpp
+++ b/src/USER-UEF/fix_nh_uef.cpp
@@ -13,19 +13,16 @@
    Contributing author: David Nicholson (MIT)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "fix_nh_uef.h"
+#include <cstring>
+#include <cmath>
 #include "atom.h"
 #include "force.h"
-#include "group.h"
 #include "comm.h"
 #include "citeme.h"
 #include "irregular.h"
 #include "modify.h"
 #include "compute.h"
-#include "kspace.h"
 #include "update.h"
 #include "domain.h"
 #include "error.h"
diff --git a/src/USER-YAFF/angle_cross.cpp b/src/USER-YAFF/angle_cross.cpp
index 2e6731f494..0f8861cdf5 100644
--- a/src/USER-YAFF/angle_cross.cpp
+++ b/src/USER-YAFF/angle_cross.cpp
@@ -15,10 +15,9 @@
    Contributing author: Steven Vandenbrande
 ------------------------------------------------------------------------- */
 
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
 #include "angle_cross.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/USER-YAFF/angle_cross.h b/src/USER-YAFF/angle_cross.h
index 7709c10414..ba958f98ec 100644
--- a/src/USER-YAFF/angle_cross.h
+++ b/src/USER-YAFF/angle_cross.h
@@ -20,7 +20,6 @@ AngleStyle(cross,AngleCross)
 #ifndef LMP_ANGLE_CROSS_H
 #define LMP_ANGLE_CROSS_H
 
-#include <stdio.h>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/USER-YAFF/angle_mm3.cpp
index 53cb11b5df..b90db37afa 100644
--- a/src/USER-YAFF/angle_mm3.cpp
+++ b/src/USER-YAFF/angle_mm3.cpp
@@ -15,10 +15,9 @@
    Contributing author: Steven Vandenbrande
 ------------------------------------------------------------------------- */
 
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
 #include "angle_mm3.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
 #include "domain.h"
diff --git a/src/USER-YAFF/angle_mm3.h b/src/USER-YAFF/angle_mm3.h
index 2d19b4d1b4..985c4bb9b4 100644
--- a/src/USER-YAFF/angle_mm3.h
+++ b/src/USER-YAFF/angle_mm3.h
@@ -20,7 +20,6 @@ AngleStyle(mm3,AngleMM3)
 #ifndef LMP_ANGLE_MM3_H
 #define LMP_ANGLE_MM3_H
 
-#include <stdio.h>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-YAFF/bond_mm3.cpp b/src/USER-YAFF/bond_mm3.cpp
index ee1ebcdd61..2a7d5d1843 100644
--- a/src/USER-YAFF/bond_mm3.cpp
+++ b/src/USER-YAFF/bond_mm3.cpp
@@ -15,12 +15,11 @@
    Contributing author: Steven Vandenbrande
 ------------------------------------------------------------------------- */
 
-#include <math.h>
-#include <stdlib.h>
 #include "bond_mm3.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/USER-YAFF/bond_mm3.h b/src/USER-YAFF/bond_mm3.h
index 9711d89529..56f3136ea8 100644
--- a/src/USER-YAFF/bond_mm3.h
+++ b/src/USER-YAFF/bond_mm3.h
@@ -20,7 +20,6 @@ BondStyle(mm3,BondMM3)
 #ifndef LMP_BOND_MM3_H
 #define LMP_BOND_MM3_H
 
-#include <stdio.h>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-YAFF/improper_distharm.cpp b/src/USER-YAFF/improper_distharm.cpp
index b45087a9ab..2b62f827e7 100644
--- a/src/USER-YAFF/improper_distharm.cpp
+++ b/src/USER-YAFF/improper_distharm.cpp
@@ -16,16 +16,14 @@
    improper_distance code by Paolo Raiteri (Curtin University)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
 #include "improper_distharm.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "domain.h"
 #include "force.h"
-#include "update.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-YAFF/improper_distharm.h b/src/USER-YAFF/improper_distharm.h
index b8b9ae780e..0a8d34ac44 100644
--- a/src/USER-YAFF/improper_distharm.h
+++ b/src/USER-YAFF/improper_distharm.h
@@ -20,7 +20,6 @@ ImproperStyle(distharm,ImproperDistHarm)
 #ifndef LMP_IMPROPER_DISTHARM_H
 #define LMP_IMPROPER_DISTHARM_H
 
-#include <stdio.h>
 #include "improper.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-YAFF/improper_sqdistharm.cpp b/src/USER-YAFF/improper_sqdistharm.cpp
index ae702820cb..bcc0549f7e 100644
--- a/src/USER-YAFF/improper_sqdistharm.cpp
+++ b/src/USER-YAFF/improper_sqdistharm.cpp
@@ -16,16 +16,14 @@
    improper_distance code by Paolo Raiteri (Curtin University)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
 #include "improper_sqdistharm.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "domain.h"
 #include "force.h"
-#include "update.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/USER-YAFF/improper_sqdistharm.h b/src/USER-YAFF/improper_sqdistharm.h
index 301b5066cb..3aceb01a03 100644
--- a/src/USER-YAFF/improper_sqdistharm.h
+++ b/src/USER-YAFF/improper_sqdistharm.h
@@ -20,7 +20,6 @@ ImproperStyle(sqdistharm,ImproperSQDistHarm)
 #ifndef LMP_IMPROPER_SQDISTHARM_H
 #define LMP_IMPROPER_SQDISTHARM_H
 
-#include <stdio.h>
 #include "improper.h"
 
 namespace LAMMPS_NS {
diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
index f37dcc3ed1..ab983a78bc 100644
--- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
+++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
@@ -15,17 +15,15 @@
    Contributing author: Steven Vandenbrande
 ------------------------------------------------------------------------- */
 
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
 #include "pair_lj_switch3_coulgauss_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
index 931ed1d116..4175ef915d 100644
--- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
+++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
@@ -15,17 +15,15 @@
    Contributing author: Steven Vandenbrande
 ------------------------------------------------------------------------- */
 
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
 #include "pair_mm3_switch3_coulgauss_long.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "neighbor.h"
 #include "neigh_list.h"
diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp
index 860126fa77..d5976f85d3 100644
--- a/src/VORONOI/compute_voronoi_atom.cpp
+++ b/src/VORONOI/compute_voronoi_atom.cpp
@@ -15,16 +15,14 @@
    Contributing author: Daniel Schwen
 ------------------------------------------------------------------------- */
 
+#include "compute_voronoi_atom.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "voro++.hh"
-#include "compute_voronoi_atom.h"
+#include <voro++.hh>
 #include "atom.h"
 #include "group.h"
 #include "update.h"
-#include "modify.h"
 #include "domain.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h
index 74bd470572..a3fff2fe16 100644
--- a/src/accelerator_kokkos.h
+++ b/src/accelerator_kokkos.h
@@ -19,14 +19,14 @@
 
 #ifdef LMP_KOKKOS
 
-#include "kokkos.h"
-#include "atom_kokkos.h"
-#include "comm_kokkos.h"
-#include "comm_tiled_kokkos.h"
-#include "domain_kokkos.h"
-#include "neighbor_kokkos.h"
-#include "memory_kokkos.h"
-#include "modify_kokkos.h"
+#include "kokkos.h"              // IWYU pragma: export
+#include "atom_kokkos.h"         // IWYU pragma: export
+#include "comm_kokkos.h"         // IWYU pragma: export
+#include "comm_tiled_kokkos.h"   // IWYU pragma: export
+#include "domain_kokkos.h"       // IWYU pragma: export
+#include "neighbor_kokkos.h"     // IWYU pragma: export
+#include "memory_kokkos.h"       // IWYU pragma: export
+#include "modify_kokkos.h"       // IWYU pragma: export
 
 #define LAMMPS_INLINE KOKKOS_INLINE_FUNCTION
 
diff --git a/src/angle.cpp b/src/angle.cpp
index 2a297990ac..1b9532ea32 100644
--- a/src/angle.cpp
+++ b/src/angle.cpp
@@ -11,7 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "angle.h"
 #include "atom.h"
 #include "comm.h"
diff --git a/src/angle.h b/src/angle.h
index ddd12ab7b8..c0d1199dcd 100644
--- a/src/angle.h
+++ b/src/angle.h
@@ -14,8 +14,7 @@
 #ifndef LMP_ANGLE_H
 #define LMP_ANGLE_H
 
-#include <cstdio>
-#include "pointers.h"
+#include "pointers.h"  // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
diff --git a/src/angle_deprecated.cpp b/src/angle_deprecated.cpp
index b5af217b7b..cc29c9978e 100644
--- a/src/angle_deprecated.cpp
+++ b/src/angle_deprecated.cpp
@@ -15,12 +15,13 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "angle_deprecated.h"
+#include <cstring>
 #include "angle_hybrid.h"
 #include "comm.h"
 #include "force.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -43,7 +44,7 @@ void AngleDeprecated::settings(int, char **)
   // hybrid substyles are created in AngleHybrid::settings(), so when this is
   // called, our style was just added at the end of the list of substyles
 
-  if (strncmp(my_style,"hybrid",6) == 0) {
+  if (utils::strmatch(my_style,"^hybrid")) {
     AngleHybrid *hybrid = (AngleHybrid *)force->angle;
     my_style = hybrid->keywords[hybrid->nstyles];
   }
diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp
index d6c616fae4..6ffbc19d08 100644
--- a/src/angle_hybrid.cpp
+++ b/src/angle_hybrid.cpp
@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
+#include "angle_hybrid.h"
+#include <mpi.h>
 #include <cstring>
 #include <cctype>
-#include "angle_hybrid.h"
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/angle_hybrid.h b/src/angle_hybrid.h
index 4fde71e43f..730d55b0e2 100644
--- a/src/angle_hybrid.h
+++ b/src/angle_hybrid.h
@@ -20,7 +20,6 @@ AngleStyle(hybrid,AngleHybrid)
 #ifndef LMP_ANGLE_HYBRID_H
 #define LMP_ANGLE_HYBRID_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp
index 6eb127fa58..3c92b852b3 100644
--- a/src/angle_zero.cpp
+++ b/src/angle_zero.cpp
@@ -15,10 +15,9 @@
    Contributing author: Carsten Svaneborg (SDU)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "angle_zero.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/angle_zero.h b/src/angle_zero.h
index b91be5c8d7..bc1ce0725f 100644
--- a/src/angle_zero.h
+++ b/src/angle_zero.h
@@ -20,7 +20,6 @@ AngleStyle(zero,AngleZero)
 #ifndef LMP_ANGLE_ZERO_H
 #define LMP_ANGLE_ZERO_H
 
-#include <cstdio>
 #include "angle.h"
 
 namespace LAMMPS_NS {
diff --git a/src/atom.cpp b/src/atom.cpp
index e5a982d620..24ad2d40da 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -11,13 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "atom.h"
 #include <mpi.h>
-#include <cmath>
-#include <cstdio>
+#include <climits>
 #include <cstdlib>
 #include <cstring>
-#include <climits>
-#include "atom.h"
 #include "style_atom.h"
 #include "atom_vec.h"
 #include "atom_vec_ellipsoid.h"
@@ -27,15 +25,12 @@
 #include "modify.h"
 #include "fix.h"
 #include "compute.h"
-#include "output.h"
-#include "thermo.h"
 #include "update.h"
 #include "domain.h"
 #include "group.h"
 #include "input.h"
 #include "variable.h"
 #include "molecule.h"
-#include "atom_masks.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/atom_map.cpp b/src/atom_map.cpp
index e9cd590624..7949e327a9 100644
--- a/src/atom_map.cpp
+++ b/src/atom_map.cpp
@@ -11,8 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "atom.h"
+#include <mpi.h>
+#include <cmath>
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp
index d4bea15d0b..bc94e36e7a 100644
--- a/src/atom_vec.cpp
+++ b/src/atom_vec.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "atom_vec.h"
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
@@ -34,6 +33,8 @@ AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp)
   mass_type = dipole_type = 0;
   forceclearflag = 0;
   size_data_bonus = 0;
+  maxexchange = 0;
+
   kokkosable = 0;
 
   nargcopy = 0;
diff --git a/src/atom_vec.h b/src/atom_vec.h
index 87fb35d9c7..2b57238c3b 100644
--- a/src/atom_vec.h
+++ b/src/atom_vec.h
@@ -14,8 +14,7 @@
 #ifndef LMP_ATOM_VEC_H
 #define LMP_ATOM_VEC_H
 
-#include <cstdio>
-#include "pointers.h"
+#include "pointers.h"  // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
@@ -39,6 +38,8 @@ class AtomVec : protected Pointers {
   int size_data_vel;                   // number of values in Velocity line
   int size_data_bonus;                 // number of values in Bonus line
   int xcol_data;                       // column (1-N) where x is in Atom line
+  int maxexchange;                     // max size of exchanged atom
+                                       // only needs to be set if size > BUFEXTRA
 
   class Molecule **onemols;            // list of molecules for style template
   int nset;                            // # of molecules in list
diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp
index af4b4e617d..25a28f1668 100644
--- a/src/atom_vec_atomic.cpp
+++ b/src/atom_vec_atomic.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_atomic.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "memory.h"
diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp
index 96cf0ec909..5e83946078 100644
--- a/src/atom_vec_body.cpp
+++ b/src/atom_vec_body.cpp
@@ -11,17 +11,16 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "atom_vec_body.h"
+#include <cstring>
+#include <string>
+#include "my_pool_chunk.h"
 #include "style_body.h"
 #include "body.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
 #include "modify.h"
-#include "force.h"
 #include "fix.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h
index 4d02c4b3e0..38309648fb 100644
--- a/src/atom_vec_body.h
+++ b/src/atom_vec_body.h
@@ -21,7 +21,6 @@ AtomStyle(body,AtomVecBody)
 #define LMP_ATOM_VEC_BODY_H
 
 #include "atom_vec.h"
-#include "my_pool_chunk.h"
 
 namespace LAMMPS_NS {
 
@@ -112,7 +111,6 @@ class AtomVecBody : public AtomVec {
 
   void grow_bonus();
   void copy_bonus(int, int);
-  //void check(int);
 };
 
 }
diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp
index fa3c99ca34..9f35d16ff0 100644
--- a/src/atom_vec_charge.cpp
+++ b/src/atom_vec_charge.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_charge.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "memory.h"
diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp
index 7bb29bd6bc..5565b82a10 100644
--- a/src/atom_vec_ellipsoid.cpp
+++ b/src/atom_vec_ellipsoid.cpp
@@ -15,12 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "atom_vec_ellipsoid.h"
+#include <cstring>
 #include "math_extra.h"
 #include "atom.h"
 #include "comm.h"
-#include "force.h"
 #include "domain.h"
 #include "modify.h"
 #include "fix.h"
diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp
index 18f6fb567d..4ca0dfbba5 100644
--- a/src/atom_vec_hybrid.cpp
+++ b/src/atom_vec_hybrid.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "atom_vec_hybrid.h"
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
-#include "force.h"
 #include "modify.h"
 #include "fix.h"
 #include "memory.h"
@@ -95,6 +93,7 @@ void AtomVecHybrid::process_args(int narg, char **arg)
   size_data_atom = 5;
   size_data_vel = 4;
   xcol_data = 3;
+  maxexchange = 0;
 
   for (int k = 0; k < nstyles; k++) {
     if ((styles[k]->molecular == 1 && molecular == 2) ||
@@ -120,6 +119,8 @@ void AtomVecHybrid::process_args(int narg, char **arg)
     size_border += styles[k]->size_border - 6;
     size_data_atom += styles[k]->size_data_atom - 5;
     size_data_vel += styles[k]->size_data_vel - 4;
+
+    maxexchange += styles[k]->maxexchange;
   }
 
   size_velocity = 3;
diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h
index a027923a17..8129baccba 100644
--- a/src/atom_vec_hybrid.h
+++ b/src/atom_vec_hybrid.h
@@ -20,7 +20,6 @@ AtomStyle(hybrid,AtomVecHybrid)
 #ifndef LMP_ATOM_VEC_HYBRID_H
 #define LMP_ATOM_VEC_HYBRID_H
 
-#include <cstdio>
 #include "atom_vec.h"
 
 namespace LAMMPS_NS {
diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp
index ba59b3d17a..695ced13fd 100644
--- a/src/atom_vec_line.cpp
+++ b/src/atom_vec_line.cpp
@@ -11,15 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "atom_vec_line.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
 #include "modify.h"
-#include "force.h"
 #include "fix.h"
 #include "math_const.h"
 #include "memory.h"
diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp
index 2a77ec418b..75136503ea 100644
--- a/src/atom_vec_sphere.cpp
+++ b/src/atom_vec_sphere.cpp
@@ -11,15 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "atom_vec_sphere.h"
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
 #include "modify.h"
-#include "force.h"
 #include "fix.h"
 #include "fix_adapt.h"
 #include "math_const.h"
diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp
index 45418b35fd..3b7bfe5377 100644
--- a/src/atom_vec_tri.cpp
+++ b/src/atom_vec_tri.cpp
@@ -11,16 +11,14 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "atom_vec_tri.h"
+#include <cmath>
+#include <cstring>
 #include "math_extra.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
 #include "modify.h"
-#include "force.h"
 #include "fix.h"
 #include "math_const.h"
 #include "memory.h"
diff --git a/src/balance.cpp b/src/balance.cpp
index 61ac895467..c3b6f7d3bf 100644
--- a/src/balance.cpp
+++ b/src/balance.cpp
@@ -18,11 +18,10 @@
 
 //#define BALANCE_DEBUG 1
 
+#include "balance.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "balance.h"
 #include "atom.h"
 #include "comm.h"
 #include "rcb.h"
@@ -30,7 +29,6 @@
 #include "domain.h"
 #include "force.h"
 #include "update.h"
-#include "group.h"
 #include "modify.h"
 #include "fix_store.h"
 #include "imbalance.h"
@@ -39,7 +37,6 @@
 #include "imbalance_neigh.h"
 #include "imbalance_store.h"
 #include "imbalance_var.h"
-#include "timer.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/balance.h b/src/balance.h
index 420031502a..424da33757 100644
--- a/src/balance.h
+++ b/src/balance.h
@@ -20,7 +20,6 @@ CommandStyle(balance,Balance)
 #ifndef LMP_BALANCE_H
 #define LMP_BALANCE_H
 
-#include <cstdio>
 #include "pointers.h"
 
 namespace LAMMPS_NS {
diff --git a/src/body.cpp b/src/body.cpp
index 78e2f5d71b..c0e58d3f4c 100644
--- a/src/body.cpp
+++ b/src/body.cpp
@@ -11,11 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "body.h"
-#include "error.h"
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/body.h b/src/body.h
index 59001620f8..8cb4039f9d 100644
--- a/src/body.h
+++ b/src/body.h
@@ -16,7 +16,6 @@
 
 #include "pointers.h"
 #include "atom_vec_body.h"
-#include "my_pool_chunk.h"
 
 namespace LAMMPS_NS {
 
@@ -28,6 +27,8 @@ class Body : protected Pointers {
   char *style;
   int size_forward;           // max extra values packed for comm
   int size_border;            // max extra values packed for border comm
+  int maxexchange;            // max size of exchanged atom
+
   AtomVecBody *avec;          // ptr to class that stores body bonus info
 
   Body(class LAMMPS *, int, char **);
diff --git a/src/bond.cpp b/src/bond.cpp
index edcd869425..bb54306280 100644
--- a/src/bond.cpp
+++ b/src/bond.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "bond.h"
+#include <mpi.h>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/bond.h b/src/bond.h
index cce94e33a0..b558a2a35e 100644
--- a/src/bond.h
+++ b/src/bond.h
@@ -14,8 +14,7 @@
 #ifndef LMP_BOND_H
 #define LMP_BOND_H
 
-#include <cstdio>
-#include "pointers.h"
+#include "pointers.h"  // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
diff --git a/src/bond_deprecated.cpp b/src/bond_deprecated.cpp
index 567b1a4d00..3e20553cac 100644
--- a/src/bond_deprecated.cpp
+++ b/src/bond_deprecated.cpp
@@ -15,8 +15,8 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "bond_deprecated.h"
+#include <cstring>
 #include "bond_hybrid.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp
index 1527943dc7..2b365014cf 100644
--- a/src/bond_hybrid.cpp
+++ b/src/bond_hybrid.cpp
@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
+#include "bond_hybrid.h"
+#include <mpi.h>
 #include <cstring>
 #include <cctype>
-#include "bond_hybrid.h"
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h
index e51d467ac1..19e4debfed 100644
--- a/src/bond_hybrid.h
+++ b/src/bond_hybrid.h
@@ -20,7 +20,6 @@ BondStyle(hybrid,BondHybrid)
 #ifndef LMP_BOND_HYBRID_H
 #define LMP_BOND_HYBRID_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp
index 0847cf9e6b..9be37c13be 100644
--- a/src/bond_zero.cpp
+++ b/src/bond_zero.cpp
@@ -15,10 +15,9 @@
    Contributing author: Carsten Svaneborg (SDU)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "bond_zero.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/bond_zero.h b/src/bond_zero.h
index 9443ff0784..7cbd2b9a96 100644
--- a/src/bond_zero.h
+++ b/src/bond_zero.h
@@ -20,7 +20,6 @@ BondStyle(zero,BondZero)
 #ifndef LMP_BOND_ZERO_H
 #define LMP_BOND_ZERO_H
 
-#include <cstdio>
 #include "bond.h"
 
 namespace LAMMPS_NS {
diff --git a/src/change_box.cpp b/src/change_box.cpp
index b7d3cb245f..98119fb3bf 100644
--- a/src/change_box.cpp
+++ b/src/change_box.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "change_box.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "change_box.h"
 #include "atom.h"
 #include "modify.h"
 #include "fix.h"
diff --git a/src/citeme.cpp b/src/citeme.cpp
index d021722671..c8745891cf 100644
--- a/src/citeme.cpp
+++ b/src/citeme.cpp
@@ -12,9 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "citeme.h"
-#include "version.h"
 #include "universe.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/citeme.h b/src/citeme.h
index 262b284337..c383ec2227 100644
--- a/src/citeme.h
+++ b/src/citeme.h
@@ -15,7 +15,6 @@
 #define LMP_CITEME_H
 
 #include "pointers.h"
-#include <cstdio>
 #include <set>
 
 namespace LAMMPS_NS {
@@ -29,7 +28,7 @@ class CiteMe : protected Pointers {
  private:
   FILE *fp;                    // opaque pointer to log.cite file object
   typedef std::set<const char *> citeset;
-  citeset *cs;                // registered set of publications
+  citeset *cs;                 // registered set of publications
 };
 
 }
diff --git a/src/comm.cpp b/src/comm.cpp
index 052de93793..fa6790e0ec 100644
--- a/src/comm.cpp
+++ b/src/comm.cpp
@@ -11,16 +11,18 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "comm.h"
 #include <mpi.h>
 #include <cstdlib>
 #include <cstring>
-#include "comm.h"
 #include "universe.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "force.h"
 #include "pair.h"
+#include "bond.h"
 #include "modify.h"
+#include "neighbor.h"
 #include "fix.h"
 #include "compute.h"
 #include "domain.h"
@@ -39,7 +41,7 @@
 
 using namespace LAMMPS_NS;
 
-#define BUFMIN 1000             // also in comm styles
+#define BUFEXTRA 1024
 
 enum{ONELEVEL,TWOLEVEL,NUMA,CUSTOM};
 enum{CART,CARTREORDER,XYZ};
@@ -65,7 +67,10 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
   outfile = NULL;
   recv_from_partition = send_to_partition = -1;
   otherflag = 0;
-  maxexchange_atom = maxexchange_fix = 0;
+
+  maxexchange = maxexchange_atom = maxexchange_fix = 0;
+  maxexchange_fix_dynamic = 0;
+  bufextra = BUFEXTRA;
 
   grid2proc = NULL;
   xsplit = ysplit = zsplit = NULL;
@@ -225,6 +230,39 @@ void Comm::init()
 
   if (force->newton == 0) maxreverse = 0;
   if (force->pair) maxreverse = MAX(maxreverse,force->pair->comm_reverse_off);
+
+  // maxexchange_atom = size of an exchanged atom, set by AtomVec
+  //   only needs to be set if size > BUFEXTRA
+  // maxexchange_fix_dynamic = 1 if any fix sets its maxexchange dynamically
+
+  maxexchange_atom = atom->avec->maxexchange;
+
+  int nfix = modify->nfix;
+  Fix **fix = modify->fix;
+
+  maxexchange_fix_dynamic = 0;
+  for (int i = 0; i < nfix; i++)
+    if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1;
+}
+
+/* ----------------------------------------------------------------------
+   set maxexchange based on AtomVec and fixes
+------------------------------------------------------------------------- */
+
+void Comm::init_exchange()
+{
+  int nfix = modify->nfix;
+  Fix **fix = modify->fix;
+
+  int onefix;
+  maxexchange_fix = 0;
+  for (int i = 0; i < nfix; i++) {
+    onefix = fix[i]->maxexchange;
+    maxexchange_fix = MAX(maxexchange_fix,onefix);
+  }
+
+  maxexchange = maxexchange_atom + maxexchange_fix;
+  bufextra = maxexchange + BUFEXTRA;
 }
 
 /* ----------------------------------------------------------------------
@@ -585,6 +623,82 @@ void Comm::set_proc_grid(int outflag)
   }
 }
 
+/* ----------------------------------------------------------------------
+   determine suitable communication cutoff.
+   this uses three inputs: 1) maximum neighborlist cutoff, 2) an estimate
+   based on bond lengths and bonded interaction styles present, and 3) a
+   user supplied communication cutoff.
+   the neighbor list cutoff (1) is *always* used, since it is a requirement
+   for neighborlists working correctly. the bond length based cutoff is
+   *only* used, if no pair style is defined and no user cutoff is provided.
+   otherwise, a warning is printed. if the bond length based estimate is
+   larger than what is used.
+   print a warning, if a user specified communication cutoff is overridden.
+------------------------------------------------------------------------- */
+
+double Comm::get_comm_cutoff()
+{
+  double maxcommcutoff, maxbondcutoff = 0.0;
+
+  if (force->bond) {
+    int n = atom->nbondtypes;
+    for (int i = 1; i <= n; ++i)
+      maxbondcutoff = MAX(maxbondcutoff,force->bond->equilibrium_distance(i));
+
+    // apply bond length based heuristics.
+
+    if (force->newton_bond) {
+      if (force->dihedral || force->improper) {
+        maxbondcutoff *= 2.25;
+      } else {
+        maxbondcutoff *=1.5;
+      }
+    } else {
+      if (force->dihedral || force->improper) {
+        maxbondcutoff *= 3.125;
+      } else if (force->angle) {
+        maxbondcutoff *= 2.25;
+      } else {
+        maxbondcutoff *=1.5;
+      }
+    }
+    maxbondcutoff += neighbor->skin;
+  }
+
+  // always take the larger of max neighbor list and user specified cutoff
+
+  maxcommcutoff = MAX(cutghostuser,neighbor->cutneighmax);
+
+  // use cutoff estimate from bond length only if no user specified
+  // cutoff was given and no pair style present. Otherwise print a
+  // warning, if the estimated bond based cutoff is larger than what
+  // is currently used.
+  
+  if (!force->pair && (cutghostuser == 0.0)) {
+    maxcommcutoff = MAX(maxcommcutoff,maxbondcutoff);
+  } else {
+    if ((me == 0) && (maxbondcutoff > maxcommcutoff)) {
+      char mesg[256];
+      snprintf(mesg,256,"Communication cutoff %g is shorter than a bond "
+               "length based estimate of %g. This may lead to errors.",
+               maxcommcutoff,maxbondcutoff);
+      error->warning(FLERR,mesg);
+    }
+  }
+
+  // print warning if neighborlist cutoff overrides user cutoff
+
+  if (me == 0) {
+    if ((cutghostuser > 0.0) && (maxcommcutoff > cutghostuser)) {
+      char mesg[128];
+      snprintf(mesg,128,"Communication cutoff adjusted to %g",maxcommcutoff);
+      error->warning(FLERR,mesg);
+    }
+  }
+
+  return maxcommcutoff;
+}
+
 /* ----------------------------------------------------------------------
    determine which proc owns atom with coord x[3] based on current decomp
    x will be in box (orthogonal) or lamda coords (triclinic)
@@ -963,11 +1077,6 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
     return 0;    // all nout_rvous are 0, no 2nd irregular
   }
 
-
-
-
-
-
   // create procs and outbuf for All2all if necesary
 
   if (!outorder) {
diff --git a/src/comm.h b/src/comm.h
index 30360b1059..d308a26367 100644
--- a/src/comm.h
+++ b/src/comm.h
@@ -14,7 +14,7 @@
 #ifndef LMP_COMM_H
 #define LMP_COMM_H
 
-#include "pointers.h"
+#include "pointers.h"  // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
@@ -38,9 +38,8 @@ class Comm : protected Pointers {
                                     // -1 if no recv or send
   int other_partition_style;        // 0 = recv layout dims must be multiple of
                                     //     my layout dims
-  int maxexchange_atom;             // max contribution to exchange from AtomVec
-  int maxexchange_fix;              // max contribution to exchange from Fixes
-  int nthreads;                     // OpenMP threads per MPI process
+
+  int nthreads;                // OpenMP threads per MPI process
 
   // public settings specific to layout = UNIFORM, NONUNIFORM
 
@@ -70,6 +69,8 @@ class Comm : protected Pointers {
   void set_processors(int, char **);      // set 3d processor grid attributes
   virtual void set_proc_grid(int outflag = 1); // setup 3d grid of procs
 
+  double get_comm_cutoff();     // determine communication cutoff
+
   virtual void setup() = 0;                      // setup 3d comm pattern
   virtual void forward_comm(int dummy = 0) = 0;  // forward comm of atom coords
   virtual void reverse_comm() = 0;               // reverse comm of forces
@@ -130,8 +131,13 @@ class Comm : protected Pointers {
   int size_reverse;                 // # of datums in reverse comm
   int size_border;                  // # of datums in forward border comm
 
-  int maxforward,maxreverse;        // max # of datums in forward/reverse comm
-  int maxexchange;                  // max # of datums/atom in exchange comm
+  int maxforward,maxreverse;    // max # of datums in forward/reverse comm
+  int maxexchange;              // max size of one exchanged atom
+  int maxexchange_atom;         // contribution to maxexchange from AtomVec
+  int maxexchange_fix;          // static contribution to maxexchange from Fixes
+  int maxexchange_fix_dynamic;  // 1 if a fix has a dynamic contribution
+  int bufextra;                 // augment send buf size for an exchange atom
+
 
   int gridflag;                     // option for creating 3d grid
   int mapflag;                      // option for mapping procs to 3d grid
@@ -147,6 +153,7 @@ class Comm : protected Pointers {
   int coregrid[3];                  // 3d grid of cores within a node
   int user_coregrid[3];             // user request for cores in each dim
 
+  void init_exchange();
   int rendezvous_irregular(int, char *, int, int, int *,
                            int (*)(int, char *, int &, int *&, char *&, void *),
                            int, char *&, int, void *, int);
@@ -237,6 +244,15 @@ Self-explanatory.
 
 E: Cannot put data on ring from NULL pointer
 
+W: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost.
+
+The communication cutoff defaults to the maximum of what is inferred from pair and
+bond styles (will be zero, if none are defined) and what is specified via
+"comm_modify cutoff" (defaults to 0.0).  If this results to 0.0, no ghost atoms will
+be generated and LAMMPS may lose atoms or use incorrect periodic images of atoms in
+interaction lists.  To avoid, either define pair style zero with a suitable cutoff
+or use comm_modify cutoff.
+
 UNDOCUMENTED
 
 U: OMP_NUM_THREADS environment is not set.
diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp
index 330551aaed..ecf382ab03 100644
--- a/src/comm_brick.cpp
+++ b/src/comm_brick.cpp
@@ -15,35 +15,25 @@
    Contributing author (triclinic) : Pieter in 't Veld (SNL)
 ------------------------------------------------------------------------- */
 
+#include "comm_brick.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdio>
-#include <cstdlib>
-#include "comm_brick.h"
-#include "comm_tiled.h"
-#include "universe.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "force.h"
 #include "pair.h"
 #include "domain.h"
 #include "neighbor.h"
-#include "group.h"
-#include "modify.h"
 #include "fix.h"
 #include "compute.h"
-#include "output.h"
 #include "dump.h"
-#include "math_extra.h"
 #include "error.h"
 #include "memory.h"
 
 using namespace LAMMPS_NS;
 
 #define BUFFACTOR 1.5
-#define BUFMIN 1000
-#define BUFEXTRA 1000
+#define BUFMIN 1024
 #define BIG 1.0e20
 
 /* ---------------------------------------------------------------------- */
@@ -110,17 +100,9 @@ void CommBrick::init_buffers()
   multilo = multihi = NULL;
   cutghostmulti = NULL;
 
-  // bufextra = max size of one exchanged atom
-  //          = allowed overflow of sendbuf in exchange()
-  // atomvec, fix reset these 2 maxexchange values if needed
-  // only necessary if their size > BUFEXTRA
-
-  maxexchange = maxexchange_atom + maxexchange_fix;
-  bufextra = maxexchange + BUFEXTRA;
-
-  maxsend = BUFMIN;
-  memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
-  maxrecv = BUFMIN;
+  buf_send = buf_recv = NULL;
+  maxsend = maxrecv = BUFMIN;
+  grow_send(maxsend,2);
   memory->create(buf_recv,maxrecv,"comm:buf_recv");
 
   nswap = 0;
@@ -141,6 +123,10 @@ void CommBrick::init()
 {
   Comm::init();
 
+  int bufextra_old = bufextra;
+  init_exchange();
+  if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
+
   // memory for multi-style communication
 
   if (mode == Comm::MULTI && multilo == NULL) {
@@ -175,7 +161,10 @@ void CommBrick::setup()
   int ntypes = atom->ntypes;
   double *prd,*sublo,*subhi;
 
-  double cut = MAX(neighbor->cutneighmax,cutghostuser);
+  double cut = get_comm_cutoff();
+  if ((cut == 0.0) && (me == 0))
+    error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms "
+                   "will be generated. Atoms may get lost.");
 
   if (triclinic == 0) {
     prd = domain->prd;
@@ -603,15 +592,14 @@ void CommBrick::exchange()
   atom->nghost = 0;
   atom->avec->clear_bonus();
 
-  // insure send buf is large enough for single atom
-  // bufextra = max size of one atom = allowed overflow of sendbuf
-  // fixes can change per-atom size requirement on-the-fly
+  // insure send buf has extra space for a single atom
+  // only need to reset if a fix can dynamically add to size of single atom
 
-  int bufextra_old = bufextra;
-  maxexchange = maxexchange_atom + maxexchange_fix;
-  bufextra = maxexchange + BUFEXTRA;
-  if (bufextra > bufextra_old)
-    grow_send(maxsend+bufextra,1);
+  if (maxexchange_fix_dynamic) {
+    int bufextra_old = bufextra;
+    init_exchange();
+    if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
+  }
 
   // subbox bounds for orthogonal or triclinic
 
@@ -1352,18 +1340,23 @@ int CommBrick::exchange_variable(int n, double *inbuf, double *&outbuf)
 
 /* ----------------------------------------------------------------------
    realloc the size of the send buffer as needed with BUFFACTOR and bufextra
-   if flag = 1, realloc
-   if flag = 0, don't need to realloc with copy, just free/malloc
+   flag = 0, don't need to realloc with copy, just free/malloc w/ BUFFACTOR
+   flag = 1, realloc with BUFFACTOR
+   flag = 2, free/malloc w/out BUFFACTOR
 ------------------------------------------------------------------------- */
 
 void CommBrick::grow_send(int n, int flag)
 {
-  maxsend = static_cast<int> (BUFFACTOR * n);
-  if (flag)
-    memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
-  else {
+  if (flag == 0) {
+    maxsend = static_cast<int> (BUFFACTOR * n);
     memory->destroy(buf_send);
     memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
+  } else if (flag == 1) {
+    maxsend = static_cast<int> (BUFFACTOR * n);
+    memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
+  } else {
+    memory->destroy(buf_send);
+    memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
   }
 }
 
diff --git a/src/comm_brick.h b/src/comm_brick.h
index b3a3a7e094..05268da63e 100644
--- a/src/comm_brick.h
+++ b/src/comm_brick.h
@@ -74,7 +74,6 @@ class CommBrick : public Comm {
   double *buf_send;                 // send buffer for all comm
   double *buf_recv;                 // recv buffer for all comm
   int maxsend,maxrecv;              // current size of send/recv buffer
-  int bufextra;                     // extra space beyond maxsend in send buffer
   int smax,rmax;             // max size in atoms of single borders send/recv
 
   // NOTE: init_buffers is called from a constructor and must not be made virtual
diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp
index d1d625445a..57b7f7e91e 100644
--- a/src/comm_tiled.cpp
+++ b/src/comm_tiled.cpp
@@ -11,19 +11,17 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "comm_tiled.h"
-#include "comm_brick.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "domain.h"
-#include "force.h"
 #include "pair.h"
 #include "neighbor.h"
-#include "modify.h"
 #include "fix.h"
 #include "compute.h"
-#include "output.h"
 #include "dump.h"
 #include "memory.h"
 #include "error.h"
@@ -32,8 +30,7 @@ using namespace LAMMPS_NS;
 
 #define BUFFACTOR 1.5
 #define BUFFACTOR 1.5
-#define BUFMIN 1000
-#define BUFEXTRA 1000
+#define BUFMIN 1024
 #define EPSILON 1.0e-6
 
 #define DELTA_PROCS 16
@@ -80,17 +77,9 @@ CommTiled::~CommTiled()
 
 void CommTiled::init_buffers()
 {
-  // bufextra = max size of one exchanged atom
-  //          = allowed overflow of sendbuf in exchange()
-  // atomvec, fix reset these 2 maxexchange values if needed
-  // only necessary if their size > BUFEXTRA
-
-  maxexchange = maxexchange_atom + maxexchange_fix;
-  bufextra = maxexchange + BUFEXTRA;
-
-  maxsend = BUFMIN;
-  memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
-  maxrecv = BUFMIN;
+  buf_send = buf_recv = NULL;
+  maxsend = maxrecv = BUFMIN;
+  grow_send(maxsend,2);
   memory->create(buf_recv,maxrecv,"comm:buf_recv");
 
   maxoverlap = 0;
@@ -108,6 +97,10 @@ void CommTiled::init()
 {
   Comm::init();
 
+  int bufextra_old = bufextra;
+  init_exchange();
+  if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
+
   // temporary restrictions
 
   if (triclinic)
@@ -157,7 +150,11 @@ void CommTiled::setup()
   // set cutoff for comm forward and comm reverse
   // check that cutoff < any periodic box length
 
-  double cut = MAX(neighbor->cutneighmax,cutghostuser);
+  double cut = get_comm_cutoff();
+  if ((cut == 0.0) && (me == 0))
+    error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms "
+                   "will be generated. Atoms may get lost.");
+
   cutghost[0] = cutghost[1] = cutghost[2] = cut;
 
   if ((periodicity[0] && cut > prd[0]) ||
@@ -644,15 +641,14 @@ void CommTiled::exchange()
   atom->nghost = 0;
   atom->avec->clear_bonus();
 
-  // insure send buf is large enough for single atom
-  // bufextra = max size of one atom = allowed overflow of sendbuf
-  // fixes can change per-atom size requirement on-the-fly
+  // insure send buf has extra space for a single atom
+  // only need to reset if a fix can dynamically add to size of single atom
 
-  int bufextra_old = bufextra;
-  maxexchange = maxexchange_atom + maxexchange_fix;
-  bufextra = maxexchange + BUFEXTRA;
-  if (bufextra > bufextra_old)
-    memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
+  if (maxexchange_fix_dynamic) {
+    int bufextra_old = bufextra;
+    init_exchange();
+    if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
+  }
 
   // domain properties used in exchange method and methods it calls
   // subbox bounds for orthogonal or triclinic
@@ -1810,18 +1806,23 @@ int CommTiled::coord2proc(double *x, int &igx, int &igy, int &igz)
 
 /* ----------------------------------------------------------------------
    realloc the size of the send buffer as needed with BUFFACTOR and bufextra
-   if flag = 1, realloc
-   if flag = 0, don't need to realloc with copy, just free/malloc
+   flag = 0, don't need to realloc with copy, just free/malloc w/ BUFFACTOR
+   flag = 1, realloc with BUFFACTOR
+   flag = 2, free/malloc w/out BUFFACTOR
 ------------------------------------------------------------------------- */
 
 void CommTiled::grow_send(int n, int flag)
 {
-  maxsend = static_cast<int> (BUFFACTOR * n);
-  if (flag)
-    memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
-  else {
+  if (flag == 0) {
+    maxsend = static_cast<int> (BUFFACTOR * n);
     memory->destroy(buf_send);
     memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
+  } else if (flag == 1) {
+    maxsend = static_cast<int> (BUFFACTOR * n);
+    memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
+  } else {
+    memory->destroy(buf_send);
+    memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
   }
 }
 
diff --git a/src/comm_tiled.h b/src/comm_tiled.h
index 13ecbc4b01..679be195aa 100644
--- a/src/comm_tiled.h
+++ b/src/comm_tiled.h
@@ -87,7 +87,6 @@ class CommTiled : public Comm {
   double *buf_send;             // send buffer for all comm
   double *buf_recv;             // recv buffer for all comm
   int maxsend,maxrecv;          // current size of send/recv buffer
-  int bufextra;                 // extra space beyond maxsend in send buffer
   int smaxone,rmaxone;          // max size in atoms of single borders send/recv
   int smaxall,rmaxall;          // max size in atoms of any borders send/recv
                                 //   for comm to all procs in one swap
diff --git a/src/compute.cpp b/src/compute.cpp
index 207f825ec8..cc92d2b5d3 100644
--- a/src/compute.cpp
+++ b/src/compute.cpp
@@ -11,15 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
+#include "compute.h"
 #include <cstring>
 #include <cctype>
-#include "compute.h"
-#include "atom.h"
 #include "domain.h"
 #include "force.h"
-#include "comm.h"
 #include "group.h"
 #include "modify.h"
 #include "fix.h"
diff --git a/src/compute.h b/src/compute.h
index a023834368..38d001db6f 100644
--- a/src/compute.h
+++ b/src/compute.h
@@ -14,7 +14,7 @@
 #ifndef LMP_COMPUTE_H
 #define LMP_COMPUTE_H
 
-#include "pointers.h"
+#include "pointers.h"  // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
diff --git a/src/compute_adf.cpp b/src/compute_adf.cpp
index e9f9ba2b6f..dee5fb214f 100644
--- a/src/compute_adf.cpp
+++ b/src/compute_adf.cpp
@@ -15,20 +15,17 @@
    Contributing authors: Aidan P. Thompson (SNL)
 ------------------------------------------------------------------------- */
 
+#include "compute_adf.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "compute_adf.h"
 #include "atom.h"
 #include "update.h"
 #include "force.h"
 #include "pair.h"
-#include "domain.h"
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "neigh_list.h"
-#include "group.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/compute_adf.h b/src/compute_adf.h
index a7983b7173..f768013207 100644
--- a/src/compute_adf.h
+++ b/src/compute_adf.h
@@ -20,7 +20,6 @@ ComputeStyle(adf,ComputeADF)
 #ifndef LMP_COMPUTE_ADF_H
 #define LMP_COMPUTE_ADF_H
 
-#include <cstdio>
 #include "compute.h"
 
 namespace LAMMPS_NS {
diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp
index 6c8c8e5d9a..e495ac6899 100644
--- a/src/compute_aggregate_atom.cpp
+++ b/src/compute_aggregate_atom.cpp
@@ -15,9 +15,10 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
+#include "compute_aggregate_atom.h"
+#include <mpi.h>
 #include <cstring>
 #include <cmath>
-#include "compute_aggregate_atom.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "update.h"
diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp
index 59945f5832..fc72a58453 100644
--- a/src/compute_angle.cpp
+++ b/src/compute_angle.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
 #include "compute_angle.h"
+#include <mpi.h>
+#include "angle.h"
 #include "update.h"
 #include "force.h"
 #include "angle_hybrid.h"
diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp
index 1196211665..b100824ea9 100644
--- a/src/compute_angle_local.cpp
+++ b/src/compute_angle_local.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_angle_local.h"
 #include <cmath>
 #include <cstring>
-#include "compute_angle_local.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp
index a70eaaf49f..05ea963b82 100644
--- a/src/compute_angmom_chunk.cpp
+++ b/src/compute_angmom_chunk.cpp
@@ -11,8 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_angmom_chunk.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp
index 896aaec9bd..5cc947c764 100644
--- a/src/compute_bond.cpp
+++ b/src/compute_bond.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
 #include "compute_bond.h"
+#include <mpi.h>
+#include "bond.h"
 #include "update.h"
 #include "force.h"
 #include "bond_hybrid.h"
diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp
index ccdd3ee77c..e14f188e62 100644
--- a/src/compute_bond_local.cpp
+++ b/src/compute_bond_local.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_bond_local.h"
 #include <cmath>
 #include <cstring>
-#include "compute_bond_local.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
@@ -33,7 +33,7 @@ using namespace LAMMPS_NS;
 #define DELTA 10000
 #define EPSILON 1.0e-12
 
-enum{DIST,VELVIB,OMEGA,ENGTRANS,ENGVIB,ENGROT,ENGPOT,FORCE,VARIABLE};
+enum{DIST,VELVIB,OMEGA,ENGTRANS,ENGVIB,ENGROT,ENGPOT,FORCE,FX,FY,FZ,VARIABLE};
 
 /* ---------------------------------------------------------------------- */
 
@@ -64,6 +64,9 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
     if (strcmp(arg[iarg],"dist") == 0) bstyle[nvalues++] = DIST;
     else if (strcmp(arg[iarg],"engpot") == 0) bstyle[nvalues++] = ENGPOT;
     else if (strcmp(arg[iarg],"force") == 0) bstyle[nvalues++] = FORCE;
+    else if (strcmp(arg[iarg],"fx") == 0) bstyle[nvalues++] = FX;
+    else if (strcmp(arg[iarg],"fy") == 0) bstyle[nvalues++] = FY;
+    else if (strcmp(arg[iarg],"fz") == 0) bstyle[nvalues++] = FZ;
     else if (strcmp(arg[iarg],"engvib") == 0) bstyle[nvalues++] = ENGVIB;
     else if (strcmp(arg[iarg],"engrot") == 0) bstyle[nvalues++] = ENGROT;
     else if (strcmp(arg[iarg],"engtrans") == 0) bstyle[nvalues++] = ENGTRANS;
@@ -127,7 +130,8 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
   singleflag = 0;
   velflag = 0;
   for (int i = 0; i < nvalues; i++) {
-    if (bstyle[i] == ENGPOT || bstyle[i] == FORCE) singleflag = 1;
+    if (bstyle[i] == ENGPOT || bstyle[i] == FORCE || bstyle[i] == FX       || 
+        bstyle[i] == FY     || bstyle[i] == FZ) singleflag = 1;
     if (bstyle[i] == VELVIB || bstyle[i] == OMEGA || bstyle[i] == ENGTRANS ||
         bstyle[i] == ENGVIB || bstyle[i] == ENGROT) velflag = 1;
   }
@@ -393,6 +397,15 @@ int ComputeBondLocal::compute_bonds(int flag)
           case FORCE:
             ptr[n] = sqrt(rsq)*fbond;
             break;
+          case FX:
+            ptr[n] = dx*fbond;
+            break;
+          case FY:
+            ptr[n] = dy*fbond;
+            break;
+          case FZ:
+            ptr[n] = dz*fbond;
+            break;
           case ENGVIB:
             ptr[n] = engvib;
             break;
diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp
index 5096879b32..18fc31390f 100644
--- a/src/compute_centro_atom.cpp
+++ b/src/compute_centro_atom.cpp
@@ -15,9 +15,8 @@
    Contributing author: Michel Perez (U Lyon) for non-fcc lattices
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "compute_centro_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp
index 61b653b375..92567101de 100644
--- a/src/compute_chunk_atom.cpp
+++ b/src/compute_chunk_atom.cpp
@@ -13,10 +13,13 @@
 
 // NOTE: allow for bin center to be variables for sphere/cylinder
 
+#include "compute_chunk_atom.h"
 #include <mpi.h>
+#include <cmath>
 #include <cstring>
 #include <cstdlib>
-#include "compute_chunk_atom.h"
+#include <map>
+#include <utility>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
@@ -24,6 +27,7 @@
 #include "region.h"
 #include "lattice.h"
 #include "modify.h"
+#include "fix.h"
 #include "fix_store.h"
 #include "comm.h"
 #include "group.h"
@@ -33,8 +37,6 @@
 #include "memory.h"
 #include "error.h"
 
-#include <map>
-
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp
index 3d0cea1add..41dbf2d5cb 100644
--- a/src/compute_chunk_spread_atom.cpp
+++ b/src/compute_chunk_spread_atom.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_chunk_spread_atom.h"
 #include <cstring>
 #include <cstdlib>
-#include "compute_chunk_spread_atom.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
@@ -23,6 +23,7 @@
 #include "input.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -116,9 +117,7 @@ ComputeChunkSpreadAtom(LAMMPS *lmp, int narg, char **arg) :
         error->all(FLERR,"Compute ID for compute chunk/spread/atom "
                    "does not exist");
 
-      char *ptr = strstr(modify->compute[icompute]->style,"/chunk");
-      if (!ptr || (ptr !=  modify->compute[icompute]->style +
-                   strlen(modify->compute[icompute]->style) - strlen("/chunk")))
+      if (!utils::strmatch(modify->compute[icompute]->style,"/chunk$"))
         error->all(FLERR,"Compute for compute chunk/spread/atom "
                    "does not calculate per-chunk values");
 
diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp
index 0c34b42671..ff227b3590 100644
--- a/src/compute_cluster_atom.cpp
+++ b/src/compute_cluster_atom.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_cluster_atom.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "compute_cluster_atom.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp
index b8ad3f0f64..054798f637 100644
--- a/src/compute_cna_atom.cpp
+++ b/src/compute_cna_atom.cpp
@@ -15,10 +15,10 @@
    Contributing author: Wan Liang (Chinese Academy of Sciences)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "compute_cna_atom.h"
+#include <mpi.h>
+#include <cstring>
+#include <cmath>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp
index ec66767245..c39911214c 100644
--- a/src/compute_com_chunk.cpp
+++ b/src/compute_com_chunk.cpp
@@ -11,8 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_com_chunk.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_contact_atom.cpp b/src/compute_contact_atom.cpp
index e60a51832a..7a288afb43 100644
--- a/src/compute_contact_atom.cpp
+++ b/src/compute_contact_atom.cpp
@@ -11,10 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
 #include "compute_contact_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
@@ -22,7 +20,6 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "force.h"
-#include "pair.h"
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp
index 54f4c70c71..30747c1314 100644
--- a/src/compute_coord_atom.cpp
+++ b/src/compute_coord_atom.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_coord_atom.h"
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "compute_coord_atom.h"
 #include "compute_orientorder_atom.h"
 #include "atom.h"
 #include "update.h"
diff --git a/src/compute_deprecated.cpp b/src/compute_deprecated.cpp
index 069fa73437..1db78b6bdf 100644
--- a/src/compute_deprecated.cpp
+++ b/src/compute_deprecated.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_deprecated.h"
+#include <cstring>
 #include "comm.h"
 #include "error.h"
 
diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp
index 3595b2eda3..e50903104a 100644
--- a/src/compute_dihedral.cpp
+++ b/src/compute_dihedral.cpp
@@ -11,11 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
 #include "compute_dihedral.h"
+#include <mpi.h>
 #include "update.h"
 #include "force.h"
+#include "dihedral.h"
 #include "dihedral_hybrid.h"
 #include "error.h"
 
diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp
index 9efdd61cb8..ac2c884c3f 100644
--- a/src/compute_dihedral_local.cpp
+++ b/src/compute_dihedral_local.cpp
@@ -11,19 +11,17 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_dihedral_local.h"
 #include <cmath>
 #include <cstring>
-#include "compute_dihedral_local.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
 #include "update.h"
 #include "domain.h"
 #include "force.h"
-#include "dihedral.h"
 #include "input.h"
 #include "variable.h"
-
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp
index b0474b6359..3790da2035 100644
--- a/src/compute_dipole_chunk.cpp
+++ b/src/compute_dipole_chunk.cpp
@@ -11,8 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_dipole_chunk.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp
index d8f279058e..41db4db1d6 100644
--- a/src/compute_displace_atom.cpp
+++ b/src/compute_displace_atom.cpp
@@ -11,15 +11,14 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_displace_atom.h"
 #include <cmath>
 #include <cstring>
-#include "compute_displace_atom.h"
 #include "atom.h"
 #include "update.h"
 #include "group.h"
 #include "domain.h"
 #include "modify.h"
-#include "fix.h"
 #include "fix_store.h"
 #include "input.h"
 #include "variable.h"
diff --git a/src/compute_erotate_sphere.cpp b/src/compute_erotate_sphere.cpp
index 31ed0aaba5..2a8588f061 100644
--- a/src/compute_erotate_sphere.cpp
+++ b/src/compute_erotate_sphere.cpp
@@ -11,14 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "compute_erotate_sphere.h"
+#include <mpi.h>
 #include "atom.h"
-#include "atom_vec.h"
 #include "update.h"
 #include "force.h"
-#include "domain.h"
-#include "group.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/compute_erotate_sphere_atom.cpp b/src/compute_erotate_sphere_atom.cpp
index 999bc062c5..78664a912f 100644
--- a/src/compute_erotate_sphere_atom.cpp
+++ b/src/compute_erotate_sphere_atom.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_erotate_sphere_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp
index bb273f3bdb..f9b68dd217 100644
--- a/src/compute_fragment_atom.cpp
+++ b/src/compute_fragment_atom.cpp
@@ -15,8 +15,9 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_fragment_atom.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "update.h"
diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp
index dc9ab52f49..15f8a8f1aa 100644
--- a/src/compute_global_atom.cpp
+++ b/src/compute_global_atom.cpp
@@ -11,17 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_global_atom.h"
 #include <cstring>
 #include <cstdlib>
-#include "compute_global_atom.h"
 #include "atom.h"
 #include "update.h"
-#include "domain.h"
 #include "modify.h"
 #include "fix.h"
-#include "force.h"
-#include "comm.h"
-#include "group.h"
 #include "input.h"
 #include "variable.h"
 #include "memory.h"
diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp
index 17e8737350..c64db19fc1 100644
--- a/src/compute_group_group.cpp
+++ b/src/compute_group_group.cpp
@@ -16,10 +16,10 @@
      K-space terms added by Stan Moore (BYU)
 ------------------------------------------------------------------------- */
 
+#include "compute_group_group.h"
 #include <mpi.h>
 #include <cstring>
 #include <cmath>
-#include "compute_group_group.h"
 #include "atom.h"
 #include "update.h"
 #include "force.h"
@@ -33,7 +33,6 @@
 #include "comm.h"
 #include "domain.h"
 #include "math_const.h"
-#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp
index 0e29c0d667..bce0c0de85 100644
--- a/src/compute_gyration.cpp
+++ b/src/compute_gyration.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "compute_gyration.h"
+#include <mpi.h>
 #include "update.h"
 #include "atom.h"
 #include "group.h"
diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp
index 6a23398aca..5677ce4b6a 100644
--- a/src/compute_gyration_chunk.cpp
+++ b/src/compute_gyration_chunk.cpp
@@ -11,9 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_gyration_chunk.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include "compute_gyration_chunk.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp
index 0b37865034..c465a2ab02 100644
--- a/src/compute_heat_flux.cpp
+++ b/src/compute_heat_flux.cpp
@@ -16,14 +16,13 @@
                          Mario Pinto (Computational Research Lab, Pune, India)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
 #include "compute_heat_flux.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "force.h"
-#include "group.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp
index 6d17ae15bd..96d4c47678 100644
--- a/src/compute_hexorder_atom.cpp
+++ b/src/compute_hexorder_atom.cpp
@@ -15,10 +15,10 @@
    Contributing author:  Aidan Thompson (SNL)
 ------------------------------------------------------------------------- */
 
-#include <complex>
-#include <cstring>
-#include <cstdlib>
 #include "compute_hexorder_atom.h"
+#include <cmath>
+#include <cstring>
+#include <complex>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp
index ac2a23e727..181771dcfb 100644
--- a/src/compute_improper.cpp
+++ b/src/compute_improper.cpp
@@ -11,11 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
 #include "compute_improper.h"
+#include <mpi.h>
 #include "update.h"
 #include "force.h"
+#include "improper.h"
 #include "improper_hybrid.h"
 #include "error.h"
 
diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp
index 2861850c79..e363749b67 100644
--- a/src/compute_improper_local.cpp
+++ b/src/compute_improper_local.cpp
@@ -11,16 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_improper_local.h"
 #include <cmath>
 #include <cstring>
-#include "compute_improper_local.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
 #include "update.h"
 #include "domain.h"
 #include "force.h"
-#include "improper.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp
index a33073c35a..be980a08ee 100644
--- a/src/compute_inertia_chunk.cpp
+++ b/src/compute_inertia_chunk.cpp
@@ -11,8 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_inertia_chunk.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_ke.cpp b/src/compute_ke.cpp
index fb3c5a9695..c6ba478dcb 100644
--- a/src/compute_ke.cpp
+++ b/src/compute_ke.cpp
@@ -11,13 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "compute_ke.h"
+#include <mpi.h>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
-#include "domain.h"
-#include "group.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/compute_ke_atom.cpp b/src/compute_ke_atom.cpp
index c5506996da..102d6364ff 100644
--- a/src/compute_ke_atom.cpp
+++ b/src/compute_ke_atom.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_ke_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp
index 608d3e6b33..b15bb8e875 100644
--- a/src/compute_msd.cpp
+++ b/src/compute_msd.cpp
@@ -11,8 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_msd.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "group.h"
diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp
index 1f974cc06c..8039a4fcd5 100644
--- a/src/compute_msd_chunk.cpp
+++ b/src/compute_msd_chunk.cpp
@@ -11,8 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_msd_chunk.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "group.h"
 #include "update.h"
diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp
index 23447da602..327c64493f 100644
--- a/src/compute_omega_chunk.cpp
+++ b/src/compute_omega_chunk.cpp
@@ -11,8 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_omega_chunk.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp
index 8a0a525fdc..0a78356127 100644
--- a/src/compute_orientorder_atom.cpp
+++ b/src/compute_orientorder_atom.cpp
@@ -16,10 +16,10 @@
                          Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
+#include "compute_orientorder_atom.h"
 #include <cstring>
 #include <cstdlib>
 #include <cmath>
-#include "compute_orientorder_atom.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
@@ -43,12 +43,14 @@ using namespace std;
   #define MY_EPSILON (10.0*2.220446049250313e-16)
 #endif
 
+#define QEPSILON 1.0e-6
+
 /* ---------------------------------------------------------------------- */
 
 ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
   qlist(NULL), distsq(NULL), nearest(NULL), rlist(NULL),
-  qnarray(NULL), qnm_r(NULL), qnm_i(NULL)
+  qnarray(NULL), qnm_r(NULL), qnm_i(NULL), cglist(NULL)
 {
   if (narg < 3 ) error->all(FLERR,"Illegal compute orientorder/atom command");
 
@@ -56,6 +58,8 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
 
   nnn = 12;
   cutsq = 0.0;
+  wlflag = 0;
+  wlhatflag = 0;
   qlcompflag = 0;
 
   // specify which orders to request
@@ -96,27 +100,39 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
       if (iarg+nqlist > narg)
         error->all(FLERR,"Illegal compute orientorder/atom command");
       qmax = 0;
-      for (int iw = 0; iw < nqlist; iw++) {
-        qlist[iw] = force->numeric(FLERR,arg[iarg+iw]);
-        if (qlist[iw] < 0)
+      for (int il = 0; il < nqlist; il++) {
+        qlist[il] = force->numeric(FLERR,arg[iarg+il]);
+        if (qlist[il] < 0)
           error->all(FLERR,"Illegal compute orientorder/atom command");
-        if (qlist[iw] > qmax) qmax = qlist[iw];
+        if (qlist[il] > qmax) qmax = qlist[il];
       }
       iarg += nqlist;
+    } else if (strcmp(arg[iarg],"wl") == 0) {
+      if (iarg+2 > narg)
+        error->all(FLERR,"Illegal compute orientorder/atom command");
+      if (strcmp(arg[iarg+1],"yes") == 0) wlflag = 1;
+      else if (strcmp(arg[iarg+1],"no") == 0) wlflag = 0;
+      else error->all(FLERR,"Illegal compute orientorder/atom command");
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"wl/hat") == 0) {
+      if (iarg+2 > narg)
+        error->all(FLERR,"Illegal compute orientorder/atom command");
+      if (strcmp(arg[iarg+1],"yes") == 0) wlhatflag = 1;
+      else if (strcmp(arg[iarg+1],"no") == 0) wlhatflag = 0;
+      else error->all(FLERR,"Illegal compute orientorder/atom command");
+      iarg += 2;
     } else if (strcmp(arg[iarg],"components") == 0) {
       qlcompflag = 1;
       if (iarg+2 > narg)
         error->all(FLERR,"Illegal compute orientorder/atom command");
       qlcomp = force->numeric(FLERR,arg[iarg+1]);
-      if (qlcomp <= 0)
-        error->all(FLERR,"Illegal compute orientorder/atom command");
       iqlcomp = -1;
-      for (int iw = 0; iw < nqlist; iw++)
-        if (qlcomp == qlist[iw]) {
-          iqlcomp = iw;
+      for (int il = 0; il < nqlist; il++)
+        if (qlcomp == qlist[il]) {
+          iqlcomp = il;
           break;
         }
-      if (iqlcomp < 0)
+      if (iqlcomp == -1)
         error->all(FLERR,"Illegal compute orientorder/atom command");
       iarg += 2;
     } else if (strcmp(arg[iarg],"cutoff") == 0) {
@@ -130,8 +146,10 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg
     } else error->all(FLERR,"Illegal compute orientorder/atom command");
   }
 
-  if (qlcompflag) ncol = nqlist + 2*(2*qlcomp+1);
-  else ncol = nqlist;
+  ncol = nqlist;
+  if (wlflag) ncol += nqlist;
+  if (wlhatflag) ncol += nqlist;
+  if (qlcompflag) ncol += 2*(2*qlcomp+1);
 
   peratom_flag = 1;
   size_peratom_cols = ncol;
@@ -151,7 +169,7 @@ ComputeOrientOrderAtom::~ComputeOrientOrderAtom()
   memory->destroy(qlist);
   memory->destroy(qnm_r);
   memory->destroy(qnm_i);
-
+  memory->destroy(cglist);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -166,8 +184,8 @@ void ComputeOrientOrderAtom::init()
     error->all(FLERR,"Compute orientorder/atom cutoff is "
                "longer than pairwise cutoff");
 
-  memory->create(qnm_r,qmax,2*qmax+1,"orientorder/atom:qnm_r");
-  memory->create(qnm_i,qmax,2*qmax+1,"orientorder/atom:qnm_i");
+  memory->create(qnm_r,nqlist,2*qmax+1,"orientorder/atom:qnm_r");
+  memory->create(qnm_i,nqlist,2*qmax+1,"orientorder/atom:qnm_i");
 
   // need an occasional full neighbor list
 
@@ -183,6 +201,8 @@ void ComputeOrientOrderAtom::init()
     if (strcmp(modify->compute[i]->style,"orientorder/atom") == 0) count++;
   if (count > 1 && comm->me == 0)
     error->warning(FLERR,"More than one compute orientorder/atom");
+
+  if (wlflag || wlhatflag) init_clebsch_gordan();
 }
 
 /* ---------------------------------------------------------------------- */
@@ -274,8 +294,8 @@ void ComputeOrientOrderAtom::compute_peratom()
       // if not nnn neighbors, order parameter = 0;
 
       if ((ncount == 0) || (ncount < nnn)) {
-        for (int iw = 0; iw < nqlist; iw++)
-          qn[iw] = 0.0;
+        for (int jj = 0; jj < ncol; jj++)
+          qn[jj] = 0.0;
         continue;
       }
 
@@ -287,6 +307,7 @@ void ComputeOrientOrderAtom::compute_peratom()
       }
 
       calc_boop(rlist, ncount, qn, qlist, nqlist);
+
     }
   }
 }
@@ -403,13 +424,12 @@ void ComputeOrientOrderAtom::select3(int k, int n, double *arr, int *iarr, doubl
 void ComputeOrientOrderAtom::calc_boop(double **rlist,
                                        int ncount, double qn[],
                                        int qlist[], int nqlist) {
-  for (int iw = 0; iw < nqlist; iw++) {
-    int n = qlist[iw];
 
-    qn[iw] = 0.0;
-    for(int m = 0; m < 2*n+1; m++) {
-      qnm_r[iw][m] = 0.0;
-      qnm_i[iw][m] = 0.0;
+  for (int il = 0; il < nqlist; il++) {
+    int l = qlist[il];
+    for(int m = 0; m < 2*l+1; m++) {
+      qnm_r[il][m] = 0.0;
+      qnm_i[il][m] = 0.0;
     }
   }
 
@@ -433,24 +453,24 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist,
       expphi_i *= rxymaginv;
     }
 
-    for (int iw = 0; iw < nqlist; iw++) {
-      int n = qlist[iw];
+    for (int il = 0; il < nqlist; il++) {
+      int l = qlist[il];
 
-      qnm_r[iw][n] += polar_prefactor(n, 0, costheta);
+      qnm_r[il][l] += polar_prefactor(l, 0, costheta);
       double expphim_r = expphi_r;
       double expphim_i = expphi_i;
-      for(int m = 1; m <= +n; m++) {
-        double prefactor = polar_prefactor(n, m, costheta);
+      for(int m = 1; m <= +l; m++) {
+        double prefactor = polar_prefactor(l, m, costheta);
         double c_r = prefactor * expphim_r;
         double c_i = prefactor * expphim_i;
-        qnm_r[iw][m+n] += c_r;
-        qnm_i[iw][m+n] += c_i;
+        qnm_r[il][m+l] += c_r;
+        qnm_i[il][m+l] += c_i;
         if(m & 1) {
-          qnm_r[iw][-m+n] -= c_r;
-          qnm_i[iw][-m+n] += c_i;
+          qnm_r[il][-m+l] -= c_r;
+          qnm_i[il][-m+l] += c_i;
         } else {
-          qnm_r[iw][-m+n] += c_r;
-          qnm_i[iw][-m+n] -= c_i;
+          qnm_r[il][-m+l] += c_r;
+          qnm_i[il][-m+l] -= c_i;
         }
         double tmp_r = expphim_r*expphi_r - expphim_i*expphi_i;
         double tmp_i = expphim_r*expphi_i + expphim_i*expphi_r;
@@ -461,30 +481,110 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist,
     }
   }
 
-  double fac = sqrt(MY_4PI) / ncount;
-  double normfac = 0.0;
-  for (int iw = 0; iw < nqlist; iw++) {
-    int n = qlist[iw];
-    double qm_sum = 0.0;
-    for(int m = 0; m < 2*n+1; m++) {
-      qm_sum += qnm_r[iw][m]*qnm_r[iw][m] + qnm_i[iw][m]*qnm_i[iw][m];
-      //      printf("Ylm^2 = %d %d %g\n",n,m,
-      //     qnm_r[iw][m]*qnm_r[iw][m] + qnm_i[iw][m]*qnm_i[iw][m]);
-    }
-    qn[iw] = fac * sqrt(qm_sum / (2*n+1));
-    if (qlcompflag && iqlcomp == iw) normfac = 1.0/sqrt(qm_sum);
+  // convert sums to averages
 
+  double facn = 1.0 / ncount;
+  for (int il = 0; il < nqlist; il++) {
+    int l = qlist[il];
+    for(int m = 0; m < 2*l+1; m++) {
+      qnm_r[il][m] *= facn;
+      qnm_i[il][m] *= facn;
+    }
   }
 
-  // output of the complex vector
+  // calculate Q_l
+  // NOTE: optional W_l_hat and components of Q_qlcomp use these stored Q_l values 
+
+  int jj = 0;
+  for (int il = 0; il < nqlist; il++) {
+    int l = qlist[il];
+    double qnormfac = sqrt(MY_4PI/(2*l+1));
+    double qm_sum = 0.0;
+    for(int m = 0; m < 2*l+1; m++)
+      qm_sum += qnm_r[il][m]*qnm_r[il][m] + qnm_i[il][m]*qnm_i[il][m];
+    qn[jj++] = qnormfac * sqrt(qm_sum);
+  }
+
+  // TODO: 
+  // 1. [done]Need to allocate extra memory in qnarray[] for this option
+  // 2. [done]Need to add keyword option
+  // 3. [done]Need to caclulate Clebsch-Gordan/Wigner 3j coefficients
+  //     (Can try getting them from boop.py first)
+  // 5. [done]Compare to bcc values in /Users/athomps/netapp/codes/MatMiner/matminer/matminer/featurizers/boop.py
+  // 6. [done]I get the right answer for W_l, but need to make sure that factor of 1/sqrt(l+1) is right for cglist
+  // 7. Add documentation
+  // 8. [done] run valgrind
+  // 9. [done] Add Wlhat
+  // 10. Update memory_usage()
+  // 11. Add exact FCC values for W_4, W_4_hat
+
+  // calculate W_l
+
+  if (wlflag) {
+    int idxcg_count = 0;
+    for (int il = 0; il < nqlist; il++) {
+      int l = qlist[il];
+      double wlsum = 0.0;
+      for(int m1 = 0; m1 < 2*l+1; m1++) {
+        for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) {
+          int m = m1 + m2 - l;
+          double qm1qm2_r = qnm_r[il][m1]*qnm_r[il][m2] - qnm_i[il][m1]*qnm_i[il][m2];
+          double qm1qm2_i = qnm_r[il][m1]*qnm_i[il][m2] + qnm_i[il][m1]*qnm_r[il][m2];
+          wlsum += (qm1qm2_r*qnm_r[il][m] + qm1qm2_i*qnm_i[il][m])*cglist[idxcg_count];
+          idxcg_count++;
+        }
+      }
+      qn[jj++] = wlsum/sqrt(2*l+1);
+    }
+  }
+
+  // calculate W_l_hat
+
+  if (wlhatflag) {
+    int idxcg_count = 0;
+    for (int il = 0; il < nqlist; il++) {
+      int l = qlist[il];
+      double wlsum = 0.0;
+      for(int m1 = 0; m1 < 2*l+1; m1++) {
+        for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) {
+          int m = m1 + m2 - l;
+          double qm1qm2_r = qnm_r[il][m1]*qnm_r[il][m2] - qnm_i[il][m1]*qnm_i[il][m2];
+          double qm1qm2_i = qnm_r[il][m1]*qnm_i[il][m2] + qnm_i[il][m1]*qnm_r[il][m2];
+          wlsum += (qm1qm2_r*qnm_r[il][m] + qm1qm2_i*qnm_i[il][m])*cglist[idxcg_count];
+          idxcg_count++;
+        }
+      }
+  //      Whats = [w/(q/np.sqrt(np.pi * 4 / (2 * l + 1)))**3 if abs(q) > 1.0e-6 else 0.0 for l,q,w in zip(range(1,max_l+1),Qs,Ws)]
+      if (qn[il] < QEPSILON)
+        qn[jj++] = 0.0;
+      else {
+        double qnormfac = sqrt(MY_4PI/(2*l+1));
+        double qnfac = qnormfac/qn[il];
+        qn[jj++] = wlsum/sqrt(2*l+1)*(qnfac*qnfac*qnfac);
+      }
+    }
+  }
+
+  // Calculate components of Q_l, for l=qlcomp
 
   if (qlcompflag) {
-    int j = nqlist;
-    for(int m = 0; m < 2*qlcomp+1; m++) {
-      qn[j++] = qnm_r[iqlcomp][m] * normfac;
-      qn[j++] = qnm_i[iqlcomp][m] * normfac;
+    int il = iqlcomp;
+    int l = qlcomp;
+    if (qn[il] < QEPSILON)
+      for(int m = 0; m < 2*l+1; m++) {
+        qn[jj++] = 0.0;
+        qn[jj++] = 0.0;
+      }
+    else {
+      double qnormfac = sqrt(MY_4PI/(2*l+1));
+      double qnfac = qnormfac/qn[il];
+      for(int m = 0; m < 2*l+1; m++) {
+        qn[jj++] = qnm_r[il][m] * qnfac;
+        qn[jj++] = qnm_i[il][m] * qnfac;
+      }
     }
   }
+
 }
 
 /* ----------------------------------------------------------------------
@@ -542,3 +642,258 @@ double ComputeOrientOrderAtom::associated_legendre(int l, int m, double x)
 
   return p;
 }
+
+/* ----------------------------------------------------------------------
+   assign Clebsch-Gordan coefficients
+   using the quasi-binomial formula VMK 8.2.1(3)
+   specialized for case j1=j2=j=l
+------------------------------------------------------------------------- */
+
+void ComputeOrientOrderAtom::init_clebsch_gordan()
+{
+  double sum,dcg,sfaccg, sfac1, sfac2;
+  int m, aa2, bb2, cc2;
+  int ifac, idxcg_count;
+
+  idxcg_count = 0;
+  for (int il = 0; il < nqlist; il++) {
+    int l = qlist[il];
+    for(int m1 = 0; m1 < 2*l+1; m1++)
+      for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++)
+        idxcg_count++;
+  }
+  idxcg_max = idxcg_count;
+  memory->create(cglist, idxcg_max, "computeorientorderatom:cglist");
+
+  idxcg_count = 0;
+  for (int il = 0; il < nqlist; il++) {
+    int l = qlist[il];
+    for(int m1 = 0; m1 < 2*l+1; m1++) {
+        aa2 = m1 - l;
+        for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) {
+          bb2 = m2 - l;
+          m = aa2 + bb2 + l;
+          
+          sum = 0.0;
+          for (int z = MAX(0, MAX(-aa2, bb2));
+               z <= MIN(l, MIN(l - aa2, l + bb2)); z++) {
+            ifac = z % 2 ? -1 : 1;
+            sum += ifac /
+              (factorial(z) *
+               factorial(l - z) *
+               factorial(l - aa2 - z) *
+               factorial(l + bb2 - z) *
+               factorial(aa2 + z) *
+               factorial(-bb2 + z));
+          }
+          
+          cc2 = m - l;
+          sfaccg = sqrt(factorial(l + aa2) *
+                        factorial(l - aa2) *
+                        factorial(l + bb2) *
+                        factorial(l - bb2) *
+                        factorial(l + cc2) *
+                        factorial(l - cc2) *
+                        (2*l + 1));
+          
+          sfac1 = factorial(3*l + 1);
+          sfac2 = factorial(l);
+          dcg = sqrt(sfac2*sfac2*sfac2 / sfac1);
+
+          cglist[idxcg_count] = sum * dcg * sfaccg;
+          idxcg_count++;
+        }
+      }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   factorial n, wrapper for precomputed table
+------------------------------------------------------------------------- */
+
+double ComputeOrientOrderAtom::factorial(int n)
+{
+  if (n < 0 || n > nmaxfactorial) {
+    char str[128];
+    sprintf(str, "Invalid argument to factorial %d", n);
+    error->all(FLERR, str);
+  }
+
+  return nfac_table[n];
+}
+
+/* ----------------------------------------------------------------------
+   factorial n table, size SNA::nmaxfactorial+1
+------------------------------------------------------------------------- */
+
+const double ComputeOrientOrderAtom::nfac_table[] = {
+  1,
+  1,
+  2,
+  6,
+  24,
+  120,
+  720,
+  5040,
+  40320,
+  362880,
+  3628800,
+  39916800,
+  479001600,
+  6227020800,
+  87178291200,
+  1307674368000,
+  20922789888000,
+  355687428096000,
+  6.402373705728e+15,
+  1.21645100408832e+17,
+  2.43290200817664e+18,
+  5.10909421717094e+19,
+  1.12400072777761e+21,
+  2.5852016738885e+22,
+  6.20448401733239e+23,
+  1.5511210043331e+25,
+  4.03291461126606e+26,
+  1.08888694504184e+28,
+  3.04888344611714e+29,
+  8.8417619937397e+30,
+  2.65252859812191e+32,
+  8.22283865417792e+33,
+  2.63130836933694e+35,
+  8.68331761881189e+36,
+  2.95232799039604e+38,
+  1.03331479663861e+40,
+  3.71993326789901e+41,
+  1.37637530912263e+43,
+  5.23022617466601e+44,
+  2.03978820811974e+46,
+  8.15915283247898e+47,
+  3.34525266131638e+49,
+  1.40500611775288e+51,
+  6.04152630633738e+52,
+  2.65827157478845e+54,
+  1.1962222086548e+56,
+  5.50262215981209e+57,
+  2.58623241511168e+59,
+  1.24139155925361e+61,
+  6.08281864034268e+62,
+  3.04140932017134e+64,
+  1.55111875328738e+66,
+  8.06581751709439e+67,
+  4.27488328406003e+69,
+  2.30843697339241e+71,
+  1.26964033536583e+73,
+  7.10998587804863e+74,
+  4.05269195048772e+76,
+  2.35056133128288e+78,
+  1.3868311854569e+80,
+  8.32098711274139e+81,
+  5.07580213877225e+83,
+  3.14699732603879e+85,
+  1.98260831540444e+87,
+  1.26886932185884e+89,
+  8.24765059208247e+90,
+  5.44344939077443e+92,
+  3.64711109181887e+94,
+  2.48003554243683e+96,
+  1.71122452428141e+98,
+  1.19785716699699e+100,
+  8.50478588567862e+101,
+  6.12344583768861e+103,
+  4.47011546151268e+105,
+  3.30788544151939e+107,
+  2.48091408113954e+109,
+  1.88549470166605e+111,
+  1.45183092028286e+113,
+  1.13242811782063e+115,
+  8.94618213078297e+116,
+  7.15694570462638e+118,
+  5.79712602074737e+120,
+  4.75364333701284e+122,
+  3.94552396972066e+124,
+  3.31424013456535e+126,
+  2.81710411438055e+128,
+  2.42270953836727e+130,
+  2.10775729837953e+132,
+  1.85482642257398e+134,
+  1.65079551609085e+136,
+  1.48571596448176e+138,
+  1.3520015276784e+140,
+  1.24384140546413e+142,
+  1.15677250708164e+144,
+  1.08736615665674e+146,
+  1.03299784882391e+148,
+  9.91677934870949e+149,
+  9.61927596824821e+151,
+  9.42689044888324e+153,
+  9.33262154439441e+155,
+  9.33262154439441e+157,
+  9.42594775983835e+159,
+  9.61446671503512e+161,
+  9.90290071648618e+163,
+  1.02990167451456e+166,
+  1.08139675824029e+168,
+  1.14628056373471e+170,
+  1.22652020319614e+172,
+  1.32464181945183e+174,
+  1.44385958320249e+176,
+  1.58824554152274e+178,
+  1.76295255109024e+180,
+  1.97450685722107e+182,
+  2.23119274865981e+184,
+  2.54355973347219e+186,
+  2.92509369349301e+188,
+  3.3931086844519e+190,
+  3.96993716080872e+192,
+  4.68452584975429e+194,
+  5.5745857612076e+196,
+  6.68950291344912e+198,
+  8.09429852527344e+200,
+  9.8750442008336e+202,
+  1.21463043670253e+205,
+  1.50614174151114e+207,
+  1.88267717688893e+209,
+  2.37217324288005e+211,
+  3.01266001845766e+213,
+  3.8562048236258e+215,
+  4.97450422247729e+217,
+  6.46685548922047e+219,
+  8.47158069087882e+221,
+  1.118248651196e+224,
+  1.48727070609069e+226,
+  1.99294274616152e+228,
+  2.69047270731805e+230,
+  3.65904288195255e+232,
+  5.01288874827499e+234,
+  6.91778647261949e+236,
+  9.61572319694109e+238,
+  1.34620124757175e+241,
+  1.89814375907617e+243,
+  2.69536413788816e+245,
+  3.85437071718007e+247,
+  5.5502938327393e+249,
+  8.04792605747199e+251,
+  1.17499720439091e+254,
+  1.72724589045464e+256,
+  2.55632391787286e+258,
+  3.80892263763057e+260,
+  5.71338395644585e+262,
+  8.62720977423323e+264,
+  1.31133588568345e+267,
+  2.00634390509568e+269,
+  3.08976961384735e+271,
+  4.78914290146339e+273,
+  7.47106292628289e+275,
+  1.17295687942641e+278,
+  1.85327186949373e+280,
+  2.94670227249504e+282,
+  4.71472363599206e+284,
+  7.59070505394721e+286,
+  1.22969421873945e+289,
+  2.0044015765453e+291,
+  3.28721858553429e+293,
+  5.42391066613159e+295,
+  9.00369170577843e+297,
+  1.503616514865e+300, // nmaxfactorial = 167
+};
+
diff --git a/src/compute_orientorder_atom.h b/src/compute_orientorder_atom.h
index d5905df63b..643875ccd0 100644
--- a/src/compute_orientorder_atom.h
+++ b/src/compute_orientorder_atom.h
@@ -33,7 +33,7 @@ class ComputeOrientOrderAtom : public Compute {
   void compute_peratom();
   double memory_usage();
   double cutsq;
-  int iqlcomp, qlcomp, qlcompflag;
+  int iqlcomp, qlcomp, qlcompflag, wlflag, wlhatflag;
   int *qlist;
   int nqlist;
 
@@ -55,6 +55,13 @@ class ComputeOrientOrderAtom : public Compute {
 
   double polar_prefactor(int, int, double);
   double associated_legendre(int, int, double);
+
+  static const int nmaxfactorial = 167;
+  static const double nfac_table[];
+  double factorial(int);
+  void init_clebsch_gordan();
+  double *cglist;                      // Clebsch-Gordan coeffs
+  int idxcg_max;
 };
 
 }
diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp
index df4f3a1ddb..e9a3faf723 100644
--- a/src/compute_pair.cpp
+++ b/src/compute_pair.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_pair.h"
 #include <mpi.h>
 #include <cstring>
 #include <cctype>
-#include "compute_pair.h"
 #include "update.h"
 #include "force.h"
 #include "pair.h"
diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp
index c356a08be9..2018d929f3 100644
--- a/src/compute_pair_local.cpp
+++ b/src/compute_pair_local.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_pair_local.h"
 #include <cmath>
 #include <cstring>
 #include <cstdlib>
-#include "compute_pair_local.h"
 #include "atom.h"
 #include "update.h"
 #include "force.h"
@@ -22,7 +22,6 @@
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "neigh_list.h"
-#include "group.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp
index 5839ec2095..fd7b74b43a 100644
--- a/src/compute_pe.cpp
+++ b/src/compute_pe.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_pe.h"
 #include <mpi.h>
 #include <cstring>
-#include "compute_pe.h"
 #include "atom.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp
index 2f1dc5650e..274e1b05a6 100644
--- a/src/compute_pe_atom.cpp
+++ b/src/compute_pe_atom.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_pe_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "comm.h"
@@ -24,7 +24,6 @@
 #include "improper.h"
 #include "kspace.h"
 #include "modify.h"
-#include "fix.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp
index 978cad0cad..cb0743a7d6 100644
--- a/src/compute_pressure.cpp
+++ b/src/compute_pressure.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_pressure.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdlib>
-#include "compute_pressure.h"
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
@@ -22,6 +21,7 @@
 #include "fix.h"
 #include "force.h"
 #include "pair.h"
+#include "pair_hybrid.h"
 #include "bond.h"
 #include "angle.h"
 #include "dihedral.h"
@@ -66,6 +66,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
 
   // process optional args
 
+  pairhybridflag = 0;
   if (narg == 4) {
     keflag = 1;
     pairflag = 1;
@@ -79,6 +80,37 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
     int iarg = 4;
     while (iarg < narg) {
       if (strcmp(arg[iarg],"ke") == 0) keflag = 1;
+      else if (strcmp(arg[iarg],"pair/hybrid") == 0) {
+        int n = strlen(arg[++iarg]) + 1;
+        if (lmp->suffix) n += strlen(lmp->suffix) + 1;
+        pstyle = new char[n];
+        strcpy(pstyle,arg[iarg++]);
+
+        nsub = 0;
+
+        if (narg > iarg) {
+          if (isdigit(arg[iarg][0])) {
+            nsub = force->inumeric(FLERR,arg[iarg]);
+            ++iarg;
+            if (nsub <= 0)
+              error->all(FLERR,"Illegal compute pressure command");
+          }
+        }
+
+        // check if pair style with and without suffix exists
+
+        pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub);
+        if (!pairhybrid && lmp->suffix) {
+          strcat(pstyle,"/");
+          strcat(pstyle,lmp->suffix);
+          pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub);
+        }
+
+        if (!pairhybrid)
+          error->all(FLERR,"Unrecognized pair style in compute pressure command");
+
+        pairhybridflag = 1;
+      }
       else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
       else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
       else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
@@ -133,6 +165,20 @@ void ComputePressure::init()
     temperature = modify->compute[icompute];
   }
 
+  // recheck if pair style with and without suffix exists
+
+  if (pairhybridflag) {
+    pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub);
+    if (!pairhybrid && lmp->suffix) {
+      strcat(pstyle,"/");
+      strcat(pstyle,lmp->suffix);
+      pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub);
+    }
+
+    if (!pairhybrid)
+      error->all(FLERR,"Unrecognized pair style in compute pressure command");
+  }
+
   // detect contributions to virial
   // vptr points to all virial[6] contributions
 
@@ -140,6 +186,7 @@ void ComputePressure::init()
   nvirial = 0;
   vptr = NULL;
 
+  if (pairhybridflag && force->pair) nvirial++;
   if (pairflag && force->pair) nvirial++;
   if (bondflag && atom->molecular && force->bond) nvirial++;
   if (angleflag && atom->molecular && force->angle) nvirial++;
@@ -152,6 +199,11 @@ void ComputePressure::init()
   if (nvirial) {
     vptr = new double*[nvirial];
     nvirial = 0;
+    if (pairhybridflag && force->pair) {
+      PairHybrid *ph = (PairHybrid *) force->pair;
+      ph->no_virial_fdotr_compute = 1;
+      vptr[nvirial++] = pairhybrid->virial;
+    }
     if (pairflag && force->pair) vptr[nvirial++] = force->pair->virial;
     if (bondflag && force->bond) vptr[nvirial++] = force->bond->virial;
     if (angleflag && force->angle) vptr[nvirial++] = force->angle->virial;
diff --git a/src/compute_pressure.h b/src/compute_pressure.h
index a59a64e634..8d0ec4aa04 100644
--- a/src/compute_pressure.h
+++ b/src/compute_pressure.h
@@ -41,10 +41,16 @@ class ComputePressure : public Compute {
   Compute *temperature;
   char *id_temp;
   double virial[6];
+  int pairhybridflag;
+  class Pair *pairhybrid;
   int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag;
   int fixflag,kspaceflag;
 
   void virial_compute(int, int);
+
+ private:
+  char *pstyle;
+  int nsub;
 };
 
 }
diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp
index 0b57840696..065e3eeb82 100644
--- a/src/compute_property_atom.cpp
+++ b/src/compute_property_atom.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_property_atom.h"
 #include <cmath>
 #include <cstring>
-#include "compute_property_atom.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp
index 489890e1cc..579c7cae3f 100644
--- a/src/compute_property_chunk.cpp
+++ b/src/compute_property_chunk.cpp
@@ -11,8 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_property_chunk.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp
index ddcf5913ca..651e1190b1 100644
--- a/src/compute_property_local.cpp
+++ b/src/compute_property_local.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_property_local.h"
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "update.h"
diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp
index d49485b4ea..501a506c98 100644
--- a/src/compute_rdf.cpp
+++ b/src/compute_rdf.cpp
@@ -15,11 +15,10 @@
    Contributing authors: Paul Crozier (SNL), Jeff Greathouse (SNL)
 ------------------------------------------------------------------------- */
 
+#include "compute_rdf.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "compute_rdf.h"
 #include "atom.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/compute_rdf.h b/src/compute_rdf.h
index 52a93a38dd..85f6ce6ad2 100644
--- a/src/compute_rdf.h
+++ b/src/compute_rdf.h
@@ -20,7 +20,6 @@ ComputeStyle(rdf,ComputeRDF)
 #ifndef LMP_COMPUTE_RDF_H
 #define LMP_COMPUTE_RDF_H
 
-#include <cstdio>
 #include "compute.h"
 
 namespace LAMMPS_NS {
diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp
index 16dc84628a..8467554faa 100644
--- a/src/compute_reduce.cpp
+++ b/src/compute_reduce.cpp
@@ -11,17 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_reduce.h"
 #include <mpi.h>
 #include <cstring>
 #include <cstdlib>
-#include "compute_reduce.h"
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
 #include "modify.h"
 #include "fix.h"
-#include "force.h"
-#include "comm.h"
 #include "group.h"
 #include "input.h"
 #include "variable.h"
diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp
index f31672ef74..3b68e20fcb 100644
--- a/src/compute_reduce_chunk.cpp
+++ b/src/compute_reduce_chunk.cpp
@@ -11,9 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <string.h>
 #include "compute_reduce_chunk.h"
+#include <mpi.h>
+#include <cstring>
+#include <cstdlib>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp
index 8e91a299e8..9074124a61 100644
--- a/src/compute_reduce_region.cpp
+++ b/src/compute_reduce_region.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "compute_reduce_region.h"
+#include <mpi.h>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp
index ac70e7dd15..67b60882f6 100644
--- a/src/compute_slice.cpp
+++ b/src/compute_slice.cpp
@@ -11,13 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_slice.h"
+#include <mpi.h>
 #include <cstdlib>
 #include <cstring>
-#include "compute_slice.h"
 #include "update.h"
 #include "modify.h"
 #include "fix.h"
-#include "group.h"
 #include "input.h"
 #include "variable.h"
 #include "memory.h"
diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp
index 5211f015ab..7c0ed9ef17 100644
--- a/src/compute_stress_atom.cpp
+++ b/src/compute_stress_atom.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "compute_stress_atom.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "comm.h"
diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp
index 70a7734593..402b84bb4b 100644
--- a/src/compute_temp.cpp
+++ b/src/compute_temp.cpp
@@ -11,14 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstring>
 #include "compute_temp.h"
+#include <mpi.h>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
 #include "domain.h"
-#include "comm.h"
 #include "group.h"
 #include "error.h"
 
diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp
index 396492e18d..0fa5bbbb8a 100644
--- a/src/compute_temp_chunk.cpp
+++ b/src/compute_temp_chunk.cpp
@@ -11,8 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_temp_chunk.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp
index c46a17497f..dc12e8f6db 100644
--- a/src/compute_temp_com.cpp
+++ b/src/compute_temp_com.cpp
@@ -11,16 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
-#include <cstring>
 #include "compute_temp_com.h"
+#include <mpi.h>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
 #include "group.h"
 #include "domain.h"
-#include "lattice.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp
index 280c17dd08..7d81a84bc4 100644
--- a/src/compute_temp_deform.cpp
+++ b/src/compute_temp_deform.cpp
@@ -15,9 +15,9 @@
    Contributing author: Pieter in 't Veld (SNL)
 ------------------------------------------------------------------------- */
 
+#include "compute_temp_deform.h"
 #include <mpi.h>
 #include <cstring>
-#include "compute_temp_deform.h"
 #include "domain.h"
 #include "atom.h"
 #include "update.h"
diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp
index ee72ba3e74..f5f29d9dc0 100644
--- a/src/compute_temp_partial.cpp
+++ b/src/compute_temp_partial.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
 #include "compute_temp_partial.h"
+#include <mpi.h>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp
index c7f0b28a6c..fce145848e 100644
--- a/src/compute_temp_profile.cpp
+++ b/src/compute_temp_profile.cpp
@@ -11,15 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
-#include <cstring>
 #include "compute_temp_profile.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
 #include "group.h"
-#include "fix.h"
 #include "domain.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp
index 36e7f51ce4..30f6701fcd 100644
--- a/src/compute_temp_ramp.cpp
+++ b/src/compute_temp_ramp.cpp
@@ -11,15 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
-#include <cstring>
 #include "compute_temp_ramp.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
 #include "group.h"
-#include "fix.h"
 #include "domain.h"
 #include "lattice.h"
 #include "memory.h"
diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp
index 0c54aeb63c..4c0b925eb6 100644
--- a/src/compute_temp_region.cpp
+++ b/src/compute_temp_region.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_temp_region.h"
 #include <mpi.h>
 #include <cstring>
-#include "compute_temp_region.h"
 #include "atom.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp
index 23e74634b5..786ef523ad 100644
--- a/src/compute_temp_sphere.cpp
+++ b/src/compute_temp_sphere.cpp
@@ -11,16 +11,14 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "compute_temp_sphere.h"
 #include <mpi.h>
 #include <cstring>
-#include "compute_temp_sphere.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "update.h"
 #include "force.h"
 #include "domain.h"
 #include "modify.h"
-#include "comm.h"
 #include "group.h"
 #include "error.h"
 
diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp
index d9de99bcb2..35eef8fe10 100644
--- a/src/compute_torque_chunk.cpp
+++ b/src/compute_torque_chunk.cpp
@@ -11,8 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_torque_chunk.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp
index d46b8b5fa0..5123e3aab4 100644
--- a/src/compute_vacf.cpp
+++ b/src/compute_vacf.cpp
@@ -11,8 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_vacf.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "group.h"
diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp
index a6dd796c63..b0a8dbeee7 100644
--- a/src/compute_vcm_chunk.cpp
+++ b/src/compute_vcm_chunk.cpp
@@ -11,13 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "compute_vcm_chunk.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "compute_chunk_atom.h"
-#include "domain.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index 52e4256fca..8a091ef2ef 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "create_atoms.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
@@ -23,8 +22,6 @@
 #include "modify.h"
 #include "force.h"
 #include "special.h"
-#include "fix.h"
-#include "compute.h"
 #include "domain.h"
 #include "lattice.h"
 #include "region.h"
@@ -176,8 +173,6 @@ void CreateAtoms::command(int narg, char **arg)
       } else error->all(FLERR,"Illegal create_atoms command");
       iarg += 3;
     } else if (strcmp(arg[iarg],"rotate") == 0) {
-      if (style != SINGLE)
-        error->all(FLERR,"Cannot use create_atoms rotate unless single style");
       if (iarg+5 > narg) error->all(FLERR,"Illegal create_atoms command");
       double thetaone;
       double axisone[3];
@@ -678,7 +673,9 @@ void CreateAtoms::add_random()
         coord[1] >= sublo[1] && coord[1] < subhi[1] &&
         coord[2] >= sublo[2] && coord[2] < subhi[2]) {
       if (mode == ATOM) atom->avec->create_atom(ntype,xone);
-      else add_molecule(xone);
+      else if (quatone[0] == 0 && quatone[1] == 0 && quatone[2] == 0)
+        add_molecule(xone);
+      else add_molecule(xone, quatone);
     }
   }
 
@@ -832,7 +829,9 @@ void CreateAtoms::add_lattice()
           // add the atom or entire molecule to my list of atoms
 
           if (mode == ATOM) atom->avec->create_atom(basistype[m],x);
-          else add_molecule(x);
+          else if (quatone[0] == 0 && quatone[1] == 0 && quatone[2] == 0)
+            add_molecule(x);
+          else add_molecule(x,quatone);
         }
       }
     }
diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index e19b565554..5b7c354595 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -15,9 +15,9 @@
    Contributing authors: Mike Salerno (NRL) added single methods
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "create_bonds.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "force.h"
diff --git a/src/create_box.cpp b/src/create_box.cpp
index b5e37b759c..4a826cb691 100644
--- a/src/create_box.cpp
+++ b/src/create_box.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "create_box.h"
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
-#include "force.h"
 #include "domain.h"
 #include "region.h"
 #include "region_prism.h"
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index 41df167f07..e8d9c5d53b 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -11,9 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "delete_atoms.h"
+#include <mpi.h>
+#include <cstring>
+#include <utility>
 #include "atom.h"
 #include "atom_vec.h"
 #include "atom_vec_ellipsoid.h"
diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp
index fe32bca879..c450f77ee7 100644
--- a/src/delete_bonds.cpp
+++ b/src/delete_bonds.cpp
@@ -11,14 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "delete_bonds.h"
 #include <mpi.h>
 #include <cstdlib>
 #include <cstring>
-#include "delete_bonds.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "domain.h"
-#include "neighbor.h"
 #include "comm.h"
 #include "force.h"
 #include "group.h"
diff --git a/src/deprecated.cpp b/src/deprecated.cpp
index b937482669..86af54fbfd 100644
--- a/src/deprecated.cpp
+++ b/src/deprecated.cpp
@@ -15,10 +15,9 @@
    Contributing authors:  Axel Kohlmeyer (Temple U),
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "deprecated.h"
+#include <cstring>
 #include "comm.h"
-#include "force.h"
 #include "error.h"
 #include "input.h"
 
diff --git a/src/dihedral.cpp b/src/dihedral.cpp
index adccf2a490..d2de841dd0 100644
--- a/src/dihedral.cpp
+++ b/src/dihedral.cpp
@@ -11,13 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "dihedral.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "pair.h"
-#include "suffix.h"
 #include "atom_masks.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/dihedral.h b/src/dihedral.h
index ac3786c40e..f7b0ad1c71 100644
--- a/src/dihedral.h
+++ b/src/dihedral.h
@@ -14,8 +14,7 @@
 #ifndef LMP_DIHEDRAL_H
 #define LMP_DIHEDRAL_H
 
-#include <cstdio>
-#include "pointers.h"
+#include "pointers.h"  // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
diff --git a/src/dihedral_deprecated.cpp b/src/dihedral_deprecated.cpp
index 70888ca76d..0205b1b887 100644
--- a/src/dihedral_deprecated.cpp
+++ b/src/dihedral_deprecated.cpp
@@ -15,8 +15,8 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "dihedral_deprecated.h"
+#include <cstring>
 #include "dihedral_hybrid.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp
index 8908139bdc..6c0a4338ae 100644
--- a/src/dihedral_hybrid.cpp
+++ b/src/dihedral_hybrid.cpp
@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
+#include "dihedral_hybrid.h"
+#include <mpi.h>
 #include <cstring>
 #include <cctype>
-#include "dihedral_hybrid.h"
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/dihedral_hybrid.h b/src/dihedral_hybrid.h
index 0839fdfc61..2804060af4 100644
--- a/src/dihedral_hybrid.h
+++ b/src/dihedral_hybrid.h
@@ -20,7 +20,6 @@ DihedralStyle(hybrid,DihedralHybrid)
 #ifndef LMP_DIHEDRAL_HYBRID_H
 #define LMP_DIHEDRAL_HYBRID_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp
index 8145d5f32d..daf46fe79a 100644
--- a/src/dihedral_zero.cpp
+++ b/src/dihedral_zero.cpp
@@ -15,13 +15,10 @@
    Contributing author: Carsten Svaneborg (SDU)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "dihedral_zero.h"
+#include <cstring>
 #include "atom.h"
 #include "force.h"
-#include "comm.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/dihedral_zero.h b/src/dihedral_zero.h
index e7dbb0d3a5..e97f8f6641 100644
--- a/src/dihedral_zero.h
+++ b/src/dihedral_zero.h
@@ -24,7 +24,6 @@ DihedralStyle(zero,DihedralZero)
 #ifndef LMP_DIHEDRAL_ZERO_H
 #define LMP_DIHEDRAL_ZERO_H
 
-#include <cstdio>
 #include "dihedral.h"
 
 namespace LAMMPS_NS {
diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp
index 7b29b1d3d5..dc94c3ed35 100644
--- a/src/displace_atoms.cpp
+++ b/src/displace_atoms.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
-#include <cstring>
 #include "displace_atoms.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "modify.h"
 #include "domain.h"
diff --git a/src/domain.cpp b/src/domain.cpp
index 74d7560c31..372b264013 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -15,12 +15,10 @@
    Contributing author (triclinic) : Pieter in 't Veld (SNL)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
-#include <cstring>
-#include <cstdio>
-#include <cmath>
 #include "domain.h"
+#include <mpi.h>
+#include <cstring>
+#include <cmath>
 #include "style_region.h"
 #include "atom.h"
 #include "atom_vec.h"
@@ -37,13 +35,11 @@
 #include "output.h"
 #include "thermo.h"
 #include "universe.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 #include "utils.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define BIG   1.0e20
 #define SMALL 1.0e-4
diff --git a/src/domain.h b/src/domain.h
index e131d07a1b..a0bda8ae72 100644
--- a/src/domain.h
+++ b/src/domain.h
@@ -15,9 +15,9 @@
 #define LMP_DOMAIN_H
 
 #include <cmath>
-#include "pointers.h"
 #include <map>
 #include <string>
+#include "pointers.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/dump.cpp b/src/dump.cpp
index 8fa07a9cb2..57a8decbb0 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -11,11 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
-#include <cstring>
-#include <cstdio>
 #include "dump.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "irregular.h"
 #include "update.h"
diff --git a/src/dump.h b/src/dump.h
index 1c6a131f76..bc7fd2d5a5 100644
--- a/src/dump.h
+++ b/src/dump.h
@@ -14,9 +14,7 @@
 #ifndef LMP_DUMP_H
 #define LMP_DUMP_H
 
-#include <mpi.h>
-#include <cstdio>
-#include "pointers.h"
+#include "pointers.h"  // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp
index 74583f4013..e2e77cfb77 100644
--- a/src/dump_atom.cpp
+++ b/src/dump_atom.cpp
@@ -11,12 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "dump_atom.h"
+#include <cstring>
 #include "domain.h"
 #include "atom.h"
 #include "update.h"
-#include "group.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp
index ddd662c8a6..3430720b8c 100644
--- a/src/dump_cfg.cpp
+++ b/src/dump_cfg.cpp
@@ -16,18 +16,10 @@
         Memory efficiency improved by Ray Shan (Sandia)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "dump_cfg.h"
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
-#include "comm.h"
-#include "modify.h"
-#include "compute.h"
-#include "input.h"
-#include "fix.h"
-#include "variable.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 17ad4b89ef..ce83e442c9 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
+#include "dump_custom.h"
 #include <cstdlib>
 #include <cstring>
-#include "dump_custom.h"
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp
index 384e9089c0..254b371e22 100644
--- a/src/dump_dcd.cpp
+++ b/src/dump_dcd.cpp
@@ -16,12 +16,10 @@
                         Axel Kohlmeyer (Temple U), support for groups
 ------------------------------------------------------------------------- */
 
+#include "dump_dcd.h"
 #include <cmath>
-#include <inttypes.h> // <cinttypes> requires C++-11
-#include <cstdio>
 #include <ctime>
 #include <cstring>
-#include "dump_dcd.h"
 #include "domain.h"
 #include "atom.h"
 #include "update.h"
diff --git a/src/dump_deprecated.cpp b/src/dump_deprecated.cpp
index f0999f4276..4263b9801f 100644
--- a/src/dump_deprecated.cpp
+++ b/src/dump_deprecated.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "dump_deprecated.h"
+#include <cstring>
 #include "comm.h"
 #include "error.h"
 
diff --git a/src/dump_image.cpp b/src/dump_image.cpp
index 0d63d2e4cb..7e6bc0c44c 100644
--- a/src/dump_image.cpp
+++ b/src/dump_image.cpp
@@ -11,20 +11,20 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "dump_image.h"
+#include <mpi.h>
 #include <cmath>
 #include <cctype>
-#include <cstdlib>
 #include <cstring>
-#include "dump_image.h"
 #include "image.h"
 #include "atom.h"
+#include "atom_vec.h"
 #include "atom_vec_line.h"
 #include "atom_vec_tri.h"
 #include "atom_vec_body.h"
 #include "body.h"
 #include "molecule.h"
 #include "domain.h"
-#include "group.h"
 #include "force.h"
 #include "comm.h"
 #include "modify.h"
diff --git a/src/dump_local.cpp b/src/dump_local.cpp
index 8dc0554690..9f021a7b6a 100644
--- a/src/dump_local.cpp
+++ b/src/dump_local.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "dump_local.h"
 #include <mpi.h>
 #include <cstring>
 #include <cstdlib>
-#include "dump_local.h"
-#include "atom.h"
 #include "modify.h"
 #include "fix.h"
 #include "compute.h"
diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp
index 59dfdc3d6e..ea67320d4a 100644
--- a/src/dump_movie.cpp
+++ b/src/dump_movie.cpp
@@ -15,13 +15,10 @@
    Contributing author:  Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "dump_movie.h"
+#include <cstring>
 #include "comm.h"
 #include "force.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp
index fd52671d81..10ba10f995 100644
--- a/src/dump_xyz.cpp
+++ b/src/dump_xyz.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "dump_xyz.h"
+#include <cstring>
 #include "atom.h"
-#include "group.h"
 #include "error.h"
 #include "memory.h"
 #include "update.h"
diff --git a/src/error.cpp b/src/error.cpp
index cc80dcb4d8..e5e9179fda 100644
--- a/src/error.cpp
+++ b/src/error.cpp
@@ -11,15 +11,18 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "error.h"
 #include <mpi.h>
 #include <cstdlib>
 #include <cstring>
-#include "error.h"
 #include "universe.h"
-#include "update.h"
 #include "output.h"
 #include "input.h"
 
+#if defined(LAMMPS_EXCEPTIONS)
+#include "update.h"
+#endif
+
 using namespace LAMMPS_NS;
 
 // helper function to truncate a string to a segment starting with "src/";
diff --git a/src/finish.cpp b/src/finish.cpp
index 1baa6d6fda..9ab97ae410 100644
--- a/src/finish.cpp
+++ b/src/finish.cpp
@@ -11,16 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "finish.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include <cstdio>
-#include "finish.h"
-#include "timer.h"
-#include "universe.h"
 #include "accelerator_kokkos.h"
-#include "accelerator_omp.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "molecule.h"
@@ -32,10 +28,10 @@
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "output.h"
 #include "memory.h"
 #include "error.h"
-#include "utils.h"
+#include "timer.h"
+#include "universe.h"
 
 #ifdef LMP_USER_OMP
 #include "modify.h"
diff --git a/src/fix.cpp b/src/fix.cpp
index 634bc2393d..d86acf0ae4 100644
--- a/src/fix.cpp
+++ b/src/fix.cpp
@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix.h"
 #include <cstring>
 #include <cctype>
-#include "fix.h"
 #include "atom.h"
 #include "group.h"
 #include "force.h"
-#include "comm.h"
 #include "atom_masks.h"
 #include "memory.h"
 #include "error.h"
@@ -78,6 +77,8 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) :
   enforce2d_flag = 0;
   respa_level_support = 0;
   respa_level = -1;
+  maxexchange = 0;
+  maxexchange_dynamic = 0;
 
   scalar_flag = vector_flag = array_flag = 0;
   peratom_flag = local_flag = 0;
diff --git a/src/fix.h b/src/fix.h
index 7eaff38bd3..bcab6f289e 100644
--- a/src/fix.h
+++ b/src/fix.h
@@ -14,7 +14,7 @@
 #ifndef LMP_FIX_H
 #define LMP_FIX_H
 
-#include "pointers.h"
+#include "pointers.h"  // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
@@ -56,6 +56,8 @@ class Fix : protected Pointers {
   int enforce2d_flag;            // 1 if has enforce2d method
   int respa_level_support;       // 1 if fix supports fix_modify respa
   int respa_level;               // which respa level to apply fix (1-Nrespa)
+  int maxexchange;               // max # of per-atom values for Comm::exchange()
+  int maxexchange_dynamic;       // 1 if fix sets maxexchange dynamically
 
   int scalar_flag;               // 0/1 if compute_scalar() function exists
   int vector_flag;               // 0/1 if compute_vector() function exists
diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp
index 9a5b528747..8668690e1d 100644
--- a/src/fix_adapt.cpp
+++ b/src/fix_adapt.cpp
@@ -11,10 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
 #include "fix_adapt.h"
+#include <cstring>
 #include "atom.h"
 #include "bond.h"
 #include "update.h"
diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp
index d66457a1f1..275ec2c846 100644
--- a/src/fix_addforce.cpp
+++ b/src/fix_addforce.cpp
@@ -11,9 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_addforce.h"
+#include <mpi.h>
 #include <cstring>
 #include <cstdlib>
-#include "fix_addforce.h"
 #include "atom.h"
 #include "atom_masks.h"
 #include "update.h"
diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp
index c8cbad75c9..694df2bcf7 100644
--- a/src/fix_ave_atom.cpp
+++ b/src/fix_ave_atom.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_ave_atom.h"
 #include <cstdlib>
 #include <cstring>
-#include "fix_ave_atom.h"
 #include "atom.h"
-#include "domain.h"
 #include "update.h"
 #include "modify.h"
 #include "compute.h"
diff --git a/src/fix_ave_atom.h b/src/fix_ave_atom.h
index e4baf6bda1..42aa282d53 100644
--- a/src/fix_ave_atom.h
+++ b/src/fix_ave_atom.h
@@ -20,7 +20,6 @@ FixStyle(ave/atom,FixAveAtom)
 #ifndef LMP_FIX_AVE_ATOM_H
 #define LMP_FIX_AVE_ATOM_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp
index 7aed4dcbe7..45eb38f5c2 100644
--- a/src/fix_ave_chunk.cpp
+++ b/src/fix_ave_chunk.cpp
@@ -11,10 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_ave_chunk.h"
+#include <mpi.h>
 #include <cstdlib>
 #include <cstring>
 #include <unistd.h>
-#include "fix_ave_chunk.h"
 #include "atom.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/fix_ave_chunk.h b/src/fix_ave_chunk.h
index 4dc1c1c246..dac5761ae8 100644
--- a/src/fix_ave_chunk.h
+++ b/src/fix_ave_chunk.h
@@ -20,7 +20,6 @@ FixStyle(ave/chunk,FixAveChunk)
 #ifndef LMP_FIX_AVE_CHUNK_H
 #define LMP_FIX_AVE_CHUNK_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp
index 5c95f20ec2..f65b53efc8 100644
--- a/src/fix_ave_correlate.cpp
+++ b/src/fix_ave_correlate.cpp
@@ -17,10 +17,11 @@
      Reese Jones (Sandia)
 ------------------------------------------------------------------------- */
 
+#include "fix_ave_correlate.h"
+#include <mpi.h>
 #include <cstdlib>
 #include <cstring>
 #include <unistd.h>
-#include "fix_ave_correlate.h"
 #include "update.h"
 #include "modify.h"
 #include "compute.h"
diff --git a/src/fix_ave_correlate.h b/src/fix_ave_correlate.h
index ff20e8ba94..05fd6b6576 100644
--- a/src/fix_ave_correlate.h
+++ b/src/fix_ave_correlate.h
@@ -20,7 +20,6 @@ FixStyle(ave/correlate,FixAveCorrelate)
 #ifndef LMP_FIX_AVE_CORRELATE_H
 #define LMP_FIX_AVE_CORRELATE_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp
index 87da5222f0..5a5de6d0b6 100644
--- a/src/fix_ave_histo.cpp
+++ b/src/fix_ave_histo.cpp
@@ -11,15 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_ave_histo.h"
+#include <mpi.h>
 #include <cstdlib>
 #include <cstring>
 #include <unistd.h>
-#include "fix_ave_histo.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "compute.h"
-#include "group.h"
 #include "input.h"
 #include "variable.h"
 #include "memory.h"
diff --git a/src/fix_ave_histo.h b/src/fix_ave_histo.h
index 3616959c61..35bdfcfa7f 100644
--- a/src/fix_ave_histo.h
+++ b/src/fix_ave_histo.h
@@ -20,7 +20,6 @@ FixStyle(ave/histo,FixAveHisto)
 #ifndef LMP_FIX_AVE_HISTO_H
 #define LMP_FIX_AVE_HISTO_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp
index c78f4fa1e3..f4ff0ae55f 100644
--- a/src/fix_ave_histo_weight.cpp
+++ b/src/fix_ave_histo_weight.cpp
@@ -14,21 +14,18 @@
 /* ----------------------------------------------------------------------
    Contributing author: Shawn Coleman (ARL)
 ------------------------------------------------------------------------- */
-
-#include <cstdlib>
-#include <cstring>
-#include <unistd.h>
 #include "fix_ave_histo_weight.h"
+#include <mpi.h>
+#include <unistd.h>
+#include "fix.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
 #include "compute.h"
-#include "group.h"
 #include "input.h"
 #include "variable.h"
 #include "memory.h"
 #include "error.h"
-#include "force.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -36,7 +33,7 @@ using namespace FixConst;
 enum{X,V,F,COMPUTE,FIX,VARIABLE};
 enum{ONE,RUNNING};
 enum{SCALAR,VECTOR,WINDOW};
-enum{GLOBAL,PERATOM,LOCAL};
+enum{DEFAULT,GLOBAL,PERATOM,LOCAL};
 enum{IGNORE,END,EXTRA};
 enum{SINGLE,VALUE};
 
diff --git a/src/fix_ave_histo_weight.h b/src/fix_ave_histo_weight.h
index e5638e1215..6ec3ba5721 100644
--- a/src/fix_ave_histo_weight.h
+++ b/src/fix_ave_histo_weight.h
@@ -20,7 +20,6 @@ FixStyle(ave/histo/weight,FixAveHistoWeight)
 #ifndef LMP_FIX_AVE_HISTO_WEIGHT_H
 #define LMP_FIX_AVE_HISTO_WEIGHT_H
 
-#include <cstdio>
 #include "fix_ave_histo.h"
 
 namespace LAMMPS_NS {
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index 50654b6561..05d556d0c8 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -15,10 +15,11 @@
    Contributing author: Pieter in 't Veld (SNL)
 ------------------------------------------------------------------------- */
 
+#include "fix_ave_time.h"
+#include <mpi.h>
 #include <cstdlib>
 #include <cstring>
 #include <unistd.h>
-#include "fix_ave_time.h"
 #include "update.h"
 #include "force.h"
 #include "modify.h"
diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h
index 62dfbad296..01228f9e55 100644
--- a/src/fix_ave_time.h
+++ b/src/fix_ave_time.h
@@ -20,7 +20,6 @@ FixStyle(ave/time,FixAveTime)
 #ifndef LMP_FIX_AVE_TIME_H
 #define LMP_FIX_AVE_TIME_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp
index 1c87ba5785..8ad07780a9 100644
--- a/src/fix_aveforce.cpp
+++ b/src/fix_aveforce.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_aveforce.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdlib>
-#include "fix_aveforce.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp
index ddaf42b49d..5ca1ec124a 100644
--- a/src/fix_balance.cpp
+++ b/src/fix_balance.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "fix_balance.h"
+#include <cstring>
 #include "balance.h"
 #include "update.h"
 #include "atom.h"
@@ -26,7 +25,6 @@
 #include "modify.h"
 #include "fix_store.h"
 #include "rcb.h"
-#include "timer.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/fix_balance.h b/src/fix_balance.h
index 64383b5950..76cbea258a 100644
--- a/src/fix_balance.h
+++ b/src/fix_balance.h
@@ -20,7 +20,6 @@ FixStyle(balance,FixBalance)
 #ifndef LMP_FIX_BALANCE_H
 #define LMP_FIX_BALANCE_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp
index a315330d14..c19ea918b4 100644
--- a/src/fix_box_relax.cpp
+++ b/src/fix_box_relax.cpp
@@ -15,10 +15,9 @@
    Contributing author: Aidan Thompson (SNL)
 ------------------------------------------------------------------------- */
 
+#include "fix_box_relax.h"
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_box_relax.h"
 #include "atom.h"
 #include "domain.h"
 #include "update.h"
diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp
index eb7a794962..855869a574 100644
--- a/src/fix_controller.cpp
+++ b/src/fix_controller.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_controller.h"
 #include <cstdlib>
 #include <cstring>
-#include "fix_controller.h"
 #include "force.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp
index 909ead3e2a..9d84c4bb62 100644
--- a/src/fix_deform.cpp
+++ b/src/fix_deform.cpp
@@ -15,10 +15,9 @@
    Contributing author: Pieter in 't Veld (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "fix_deform.h"
+#include <cstring>
+#include <cmath>
 #include "atom.h"
 #include "update.h"
 #include "comm.h"
diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp
index 7db27152ba..0c212668b3 100644
--- a/src/fix_deprecated.cpp
+++ b/src/fix_deprecated.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_deprecated.h"
+#include <cstring>
 #include "comm.h"
 #include "error.h"
 
diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp
index e4cf12d1ff..9af5a37675 100644
--- a/src/fix_drag.cpp
+++ b/src/fix_drag.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_drag.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "respa.h"
diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp
index 7566094b48..da4bdad827 100644
--- a/src/fix_dt_reset.cpp
+++ b/src/fix_dt_reset.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_dt_reset.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "integrate.h"
diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp
index 986ded5d16..3edd24e9af 100644
--- a/src/fix_enforce2d.cpp
+++ b/src/fix_enforce2d.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_enforce2d.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
diff --git a/src/fix_external.cpp b/src/fix_external.cpp
index b1ffa65e49..afb420df93 100644
--- a/src/fix_external.cpp
+++ b/src/fix_external.cpp
@@ -11,10 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
-#include <cstdlib>
 #include "fix_external.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "memory.h"
diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp
index bc10eb2807..14ba913c01 100644
--- a/src/fix_gravity.cpp
+++ b/src/fix_gravity.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "fix_gravity.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
diff --git a/src/fix_group.cpp b/src/fix_group.cpp
index 8a332bed95..d2eea9f781 100644
--- a/src/fix_group.cpp
+++ b/src/fix_group.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_group.h"
+#include <cstring>
 #include "group.h"
 #include "update.h"
 #include "atom.h"
diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp
index 5fda4c30d6..8ebb39f0e9 100644
--- a/src/fix_halt.cpp
+++ b/src/fix_halt.cpp
@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_halt.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "update.h"
 #include "force.h"
-#include "update.h"
 #include "input.h"
 #include "variable.h"
 #include "atom.h"
diff --git a/src/fix_halt.h b/src/fix_halt.h
index 372c915a7f..93c5e95078 100644
--- a/src/fix_halt.h
+++ b/src/fix_halt.h
@@ -20,7 +20,6 @@ FixStyle(halt,FixHalt)
 #ifndef LMP_FIX_HALT_H
 #define LMP_FIX_HALT_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp
index f34845785c..67d445df92 100644
--- a/src/fix_heat.cpp
+++ b/src/fix_heat.cpp
@@ -15,10 +15,10 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_heat.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "region.h"
diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp
index b8e07dfd53..04837ff39b 100644
--- a/src/fix_indent.cpp
+++ b/src/fix_indent.cpp
@@ -15,10 +15,10 @@
    Contributing author: Ravi Agrawal (Northwestern U)
 ------------------------------------------------------------------------- */
 
+#include "fix_indent.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_indent.h"
 #include "atom.h"
 #include "input.h"
 #include "variable.h"
@@ -26,7 +26,6 @@
 #include "lattice.h"
 #include "update.h"
 #include "modify.h"
-#include "output.h"
 #include "respa.h"
 #include "error.h"
 #include "force.h"
diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp
index 3f2ec20db0..a050e5a13a 100644
--- a/src/fix_langevin.cpp
+++ b/src/fix_langevin.cpp
@@ -16,11 +16,10 @@
                          Aidan Thompson (SNL) GJF formulation
 ------------------------------------------------------------------------- */
 
+#include "fix_langevin.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_langevin.h"
 #include "math_extra.h"
 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
@@ -28,8 +27,6 @@
 #include "update.h"
 #include "modify.h"
 #include "compute.h"
-#include "domain.h"
-#include "region.h"
 #include "respa.h"
 #include "comm.h"
 #include "input.h"
diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp
index aea1a2a25b..c153ee65dd 100644
--- a/src/fix_lineforce.cpp
+++ b/src/fix_lineforce.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_lineforce.h"
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_lineforce.h"
 #include "atom.h"
 #include "update.h"
 #include "respa.h"
diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp
index fa39643a1b..93b13fac49 100644
--- a/src/fix_minimize.cpp
+++ b/src/fix_minimize.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "fix_minimize.h"
 #include "atom.h"
 #include "domain.h"
 #include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -44,8 +42,10 @@ FixMinimize::~FixMinimize()
   // delete locally stored data
 
   memory->destroy(peratom);
-  for (int m = 0; m < nvector; m++) memory->destroy(vectors[m]);
-  memory->sfree(vectors);
+  if (vectors) {
+    for (int m = 0; m < nvector; m++) memory->destroy(vectors[m]);
+    memory->sfree(vectors);
+  }
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/fix_minimize.h b/src/fix_minimize.h
index 7b9f571628..615eb6a095 100644
--- a/src/fix_minimize.h
+++ b/src/fix_minimize.h
@@ -29,22 +29,22 @@ class FixMinimize : public Fix {
 
  public:
   FixMinimize(class LAMMPS *, int, char **);
-  ~FixMinimize();
+  virtual ~FixMinimize();
   int setmask();
-  void init() {}
+  virtual void init() {}
 
   double memory_usage();
-  void grow_arrays(int);
-  void copy_arrays(int, int, int);
-  int pack_exchange(int, double *);
-  int unpack_exchange(int, double *);
+  virtual void grow_arrays(int);
+  virtual void copy_arrays(int, int, int);
+  virtual int pack_exchange(int, double *);
+  virtual int unpack_exchange(int, double *);
 
-  void add_vector(int);
+  virtual void add_vector(int);
   double *request_vector(int);
   void store_box();
   void reset_coords();
 
- private:
+ protected:
   int nvector;
   int *peratom;
   double **vectors;
diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp
index 680251e670..a363cb8eac 100644
--- a/src/fix_momentum.cpp
+++ b/src/fix_momentum.cpp
@@ -11,9 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_momentum.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "group.h"
diff --git a/src/fix_move.cpp b/src/fix_move.cpp
index 0a5f506ab2..770c0fca6b 100644
--- a/src/fix_move.cpp
+++ b/src/fix_move.cpp
@@ -11,12 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "fix_move.h"
+#include <cstring>
+#include <cmath>
 #include "atom.h"
-#include "group.h"
 #include "update.h"
 #include "modify.h"
 #include "force.h"
diff --git a/src/fix_move.h b/src/fix_move.h
index 5993d7d6e8..740b051be0 100644
--- a/src/fix_move.h
+++ b/src/fix_move.h
@@ -20,7 +20,6 @@ FixStyle(move,FixMove)
 #ifndef LMP_FIX_MOVE_H
 #define LMP_FIX_MOVE_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp
index 207c409596..673e2b1c06 100644
--- a/src/fix_neigh_history.cpp
+++ b/src/fix_neigh_history.cpp
@@ -11,18 +11,16 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_neigh_history.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdio>
-#include "fix_neigh_history.h"
+#include "my_page.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "force.h"
 #include "pair.h"
-#include "update.h"
-#include "modify.h"
 #include "memory.h"
 #include "error.h"
 
@@ -42,6 +40,7 @@ FixNeighHistory::FixNeighHistory(LAMMPS *lmp, int narg, char **arg) :
 
   restart_peratom = 1;
   create_attribute = 1;
+  maxexchange_dynamic = 1;
 
   newton_pair = force->newton_pair;
 
@@ -296,11 +295,11 @@ void FixNeighHistory::pre_exchange_onesided()
   }
 
   // set maxpartner = max # of partners of any owned atom
-  // bump up comm->maxexchange_fix if necessary
+  // maxexchange = max # of values for any Comm::exchange() atom
 
   maxpartner = 0;
   for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]);
-  comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
+  maxexchange = (dnum+1)*maxpartner + 1;
 
   // zero npartner values from previous nlocal_neigh to current nlocal
 
@@ -424,11 +423,11 @@ void FixNeighHistory::pre_exchange_newton()
   comm->reverse_comm_fix_variable(this);
 
   // set maxpartner = max # of partners of any owned atom
-  // bump up comm->maxexchange_fix if necessary
+  // maxexchange = max # of values for any Comm::exchange() atom
 
   maxpartner = 0;
   for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]);
-  comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
+  maxexchange = (dnum+1)*maxpartner + 1;
 
   // zero npartner values from previous nlocal_neigh to current nlocal
 
@@ -531,11 +530,11 @@ void FixNeighHistory::pre_exchange_no_newton()
   }
 
   // set maxpartner = max # of partners of any owned atom
-  // bump up comm->maxexchange_fix if necessary
+  // maxexchange = max # of values for any Comm::exchange() atom
 
   maxpartner = 0;
   for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]);
-  comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
+  maxexchange = (dnum+1)*maxpartner + 1;
 
   // zero npartner values from previous nlocal_neigh to current nlocal
 
@@ -796,9 +795,6 @@ void FixNeighHistory::unpack_reverse_comm(int n, int *list, double *buf)
 
 int FixNeighHistory::pack_exchange(int i, double *buf)
 {
-  // NOTE: how do I know comm buf is big enough if extreme # of touching neighs
-  // Comm::BUFEXTRA may need to be increased
-
   int m = 0;
   buf[m++] = npartner[i];
   for (int n = 0; n < npartner[i]; n++) {
diff --git a/src/fix_neigh_history.h b/src/fix_neigh_history.h
index 601e8a55a2..51d03f5b12 100644
--- a/src/fix_neigh_history.h
+++ b/src/fix_neigh_history.h
@@ -21,7 +21,6 @@ FixStyle(NEIGH_HISTORY,FixNeighHistory)
 #define LMP_FIX_NEIGH_HISTORY_H
 
 #include "fix.h"
-#include "my_page.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp
index deca0ad83d..bb3fe7559c 100644
--- a/src/fix_nh.cpp
+++ b/src/fix_nh.cpp
@@ -15,11 +15,9 @@
    Contributing authors: Mark Stevens (SNL), Aidan Thompson (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "fix_nh.h"
-#include "math_extra.h"
+#include <cstring>
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "group.h"
diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp
index f176493242..1ff3fc2d4d 100644
--- a/src/fix_nh_sphere.cpp
+++ b/src/fix_nh_sphere.cpp
@@ -15,11 +15,11 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "fix_nh_sphere.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
-#include "group.h"
 #include "error.h"
 #include "force.h"
 #include "domain.h"
diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp
index 40265ef57c..7148b024de 100644
--- a/src/fix_nph.cpp
+++ b/src/fix_nph.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nph.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp
index 3fcbe5e9c6..f64f144f34 100644
--- a/src/fix_nph_sphere.cpp
+++ b/src/fix_nph_sphere.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nph_sphere.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp
index d17577d68d..e856fafe2d 100644
--- a/src/fix_npt.cpp
+++ b/src/fix_npt.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_npt.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp
index 50ac990daf..9cbb17b0ca 100644
--- a/src/fix_npt_sphere.cpp
+++ b/src/fix_npt_sphere.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_npt_sphere.h"
+#include <cstring>
 #include "modify.h"
 #include "error.h"
 
diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp
index 959483230e..863ce5404d 100644
--- a/src/fix_nve.cpp
+++ b/src/fix_nve.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
 #include "fix_nve.h"
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp
index 68ff0665a1..d63c736e73 100644
--- a/src/fix_nve_limit.cpp
+++ b/src/fix_nve_limit.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "fix_nve_limit.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp
index d4fca9e676..022e8abe74 100644
--- a/src/fix_nve_noforce.cpp
+++ b/src/fix_nve_noforce.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_noforce.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "respa.h"
diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp
index 0bee8b8685..c0fea17c2b 100644
--- a/src/fix_nve_sphere.cpp
+++ b/src/fix_nve_sphere.cpp
@@ -11,15 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstring>
 #include "fix_nve_sphere.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "domain.h"
 #include "atom_vec.h"
-#include "update.h"
-#include "respa.h"
 #include "force.h"
 #include "error.h"
 #include "math_vector.h"
diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp
index 7247612dd4..6f0d4c6c50 100644
--- a/src/fix_nvt.cpp
+++ b/src/fix_nvt.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nvt.h"
+#include <cstring>
 #include "group.h"
 #include "modify.h"
 #include "error.h"
diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp
index c7d23364a7..138794862a 100644
--- a/src/fix_nvt_sllod.cpp
+++ b/src/fix_nvt_sllod.cpp
@@ -15,9 +15,8 @@
    Contributing author: Pieter in 't Veld (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstring>
 #include "fix_nvt_sllod.h"
+#include <cstring>
 #include "math_extra.h"
 #include "atom.h"
 #include "domain.h"
diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp
index 44046699ba..fed3799011 100644
--- a/src/fix_nvt_sphere.cpp
+++ b/src/fix_nvt_sphere.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nvt_sphere.h"
+#include <cstring>
 #include "group.h"
 #include "modify.h"
 #include "error.h"
diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp
index 45dc782fcf..a3f27277bd 100644
--- a/src/fix_planeforce.cpp
+++ b/src/fix_planeforce.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_planeforce.h"
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_planeforce.h"
 #include "atom.h"
 #include "update.h"
 #include "respa.h"
diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp
index 95db004436..c090c554e2 100644
--- a/src/fix_press_berendsen.cpp
+++ b/src/fix_press_berendsen.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "fix_press_berendsen.h"
+#include <cstring>
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
@@ -23,7 +22,6 @@
 #include "compute.h"
 #include "kspace.h"
 #include "update.h"
-#include "respa.h"
 #include "domain.h"
 #include "error.h"
 
diff --git a/src/fix_print.cpp b/src/fix_print.cpp
index f6db88114a..dc76fc39f9 100644
--- a/src/fix_print.cpp
+++ b/src/fix_print.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_print.h"
+#include <mpi.h>
+#include <cstring>
 #include "update.h"
 #include "input.h"
 #include "modify.h"
diff --git a/src/fix_print.h b/src/fix_print.h
index 37b6680aee..5644160220 100644
--- a/src/fix_print.h
+++ b/src/fix_print.h
@@ -20,7 +20,6 @@ FixStyle(print,FixPrint)
 #ifndef LMP_FIX_PRINT_H
 #define LMP_FIX_PRINT_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp
index c89419f850..555114e4f9 100644
--- a/src/fix_property_atom.cpp
+++ b/src/fix_property_atom.cpp
@@ -11,16 +11,14 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_property_atom.h"
 #include <cstdlib>
 #include <cstring>
-#include "fix_property_atom.h"
 #include "atom.h"
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
 
-#include "update.h"
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp
index 3c3178f4af..afedf9c12c 100644
--- a/src/fix_read_restart.cpp
+++ b/src/fix_read_restart.cpp
@@ -11,7 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "fix_read_restart.h"
 #include "atom.h"
 #include "memory.h"
diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp
index 75b383d67a..f461e0fa52 100644
--- a/src/fix_recenter.cpp
+++ b/src/fix_recenter.cpp
@@ -15,9 +15,9 @@
    Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_recenter.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "group.h"
 #include "update.h"
diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp
index 64461ba7ca..742dd5c58b 100644
--- a/src/fix_respa.cpp
+++ b/src/fix_respa.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_respa.h"
+#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp
index 08485d65b3..5a0d4fb662 100644
--- a/src/fix_restrain.cpp
+++ b/src/fix_restrain.cpp
@@ -16,17 +16,16 @@
      support for bond and angle restraints by Andres Jaramillo-Botero (Caltech)
 ------------------------------------------------------------------------- */
 
+#include "fix_restrain.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
-#include <cstdlib>
-#include "fix_restrain.h"
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "domain.h"
 #include "comm.h"
 #include "respa.h"
-#include "input.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp
index fc8b7aeb59..77c4bfbddc 100644
--- a/src/fix_setforce.cpp
+++ b/src/fix_setforce.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "fix_setforce.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp
index 328a0eeafd..510b194ab7 100644
--- a/src/fix_spring.cpp
+++ b/src/fix_spring.cpp
@@ -15,14 +15,12 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_spring.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "respa.h"
-#include "domain.h"
 #include "force.h"
 #include "group.h"
 #include "error.h"
diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp
index 5b5d95b111..e14936a976 100644
--- a/src/fix_spring_chunk.cpp
+++ b/src/fix_spring_chunk.cpp
@@ -11,15 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_spring_chunk.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
 #include "respa.h"
-#include "domain.h"
 #include "modify.h"
 #include "compute_chunk_atom.h"
 #include "compute_com_chunk.h"
diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp
index 28c8969006..f1e68bffa4 100644
--- a/src/fix_spring_rg.cpp
+++ b/src/fix_spring_rg.cpp
@@ -16,10 +16,8 @@
                         Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_spring_rg.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "group.h"
diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp
index 670883af41..c94f21b492 100644
--- a/src/fix_spring_self.cpp
+++ b/src/fix_spring_self.cpp
@@ -15,9 +15,9 @@
    Contributing author: Naveen Michaud-Agrawal (Johns Hopkins University)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_spring_self.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "domain.h"
diff --git a/src/fix_store.cpp b/src/fix_store.cpp
index 9db65d0987..80ffee2ded 100644
--- a/src/fix_store.cpp
+++ b/src/fix_store.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_store.h"
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -106,6 +105,7 @@ vstore(NULL), astore(NULL), rbuf(NULL)
       for (int i = 0; i < nlocal; i++)
         for (int j = 0; j < nvalues; j++)
           astore[i][j] = 0.0;
+    maxexchange = nvalues;
   }
 }
 
diff --git a/src/fix_store.h b/src/fix_store.h
index 5524770a97..437c14f0f7 100644
--- a/src/fix_store.h
+++ b/src/fix_store.h
@@ -20,7 +20,6 @@ FixStyle(STORE,FixStore)
 #ifndef LMP_FIX_STORE_H
 #define LMP_FIX_STORE_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp
index a841714098..5c25f0e162 100644
--- a/src/fix_store_force.cpp
+++ b/src/fix_store_force.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_store_force.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
-#include "group.h"
 #include "respa.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp
index da899a173c..18dfa026d9 100644
--- a/src/fix_store_state.cpp
+++ b/src/fix_store_state.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "fix_store_state.h"
 #include <cstdlib>
 #include <cstring>
-#include "fix_store_state.h"
 #include "atom.h"
 #include "domain.h"
 #include "update.h"
diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp
index 55518015c4..be8922be4e 100644
--- a/src/fix_temp_berendsen.cpp
+++ b/src/fix_temp_berendsen.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "fix_temp_berendsen.h"
+#include <cstring>
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/fix_temp_csld.cpp b/src/fix_temp_csld.cpp
index 7bdf776355..f827c88f51 100644
--- a/src/fix_temp_csld.cpp
+++ b/src/fix_temp_csld.cpp
@@ -15,10 +15,9 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "fix_temp_csld.h"
+#include <cstring>
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp
index 495a155113..55cbb60407 100644
--- a/src/fix_temp_csvr.cpp
+++ b/src/fix_temp_csvr.cpp
@@ -16,13 +16,12 @@
    Based on code by Paolo Raiteri (Curtin U) and Giovanni Bussi (SISSA)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "fix_temp_csvr.h"
+#include <mpi.h>
+#include <cstring>
+#include <cmath>
 #include "atom.h"
 #include "force.h"
-#include "memory.h"
 #include "comm.h"
 #include "input.h"
 #include "variable.h"
diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp
index 11dfa6a5fc..a9d605d5ba 100644
--- a/src/fix_temp_rescale.cpp
+++ b/src/fix_temp_rescale.cpp
@@ -11,16 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
-#include <cmath>
 #include "fix_temp_rescale.h"
+#include <cstring>
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "group.h"
 #include "update.h"
-#include "domain.h"
-#include "region.h"
 #include "comm.h"
 #include "input.h"
 #include "variable.h"
diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp
index 10315a750d..cfe9a9572e 100644
--- a/src/fix_tmd.cpp
+++ b/src/fix_tmd.cpp
@@ -16,11 +16,10 @@
                          Christian Burisch (Bochum Univeristy, Germany)
 ------------------------------------------------------------------------- */
 
+#include "fix_tmd.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "fix_tmd.h"
 #include "atom.h"
 #include "update.h"
 #include "modify.h"
diff --git a/src/fix_tmd.h b/src/fix_tmd.h
index b6db41dd5a..f23a64a027 100644
--- a/src/fix_tmd.h
+++ b/src/fix_tmd.h
@@ -20,7 +20,6 @@ FixStyle(tmd,FixTMD)
 #ifndef LMP_FIX_TMD_H
 #define LMP_FIX_TMD_H
 
-#include <cstdio>
 #include "fix.h"
 
 namespace LAMMPS_NS {
diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp
index 6387af7676..53093acbf6 100644
--- a/src/fix_vector.cpp
+++ b/src/fix_vector.cpp
@@ -11,13 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_vector.h"
+#include <cstdlib>
+#include <cstring>
 #include "update.h"
 #include "force.h"
 #include "modify.h"
 #include "compute.h"
-#include "group.h"
 #include "input.h"
 #include "variable.h"
 #include "memory.h"
diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp
index e845142322..bdd1e19976 100644
--- a/src/fix_viscous.cpp
+++ b/src/fix_viscous.cpp
@@ -11,10 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_viscous.h"
+#include <cstring>
 #include "atom.h"
 #include "update.h"
 #include "respa.h"
diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp
index e84d01191d..a30b14c231 100644
--- a/src/fix_wall.cpp
+++ b/src/fix_wall.cpp
@@ -11,11 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_wall.h"
-#include "atom.h"
+#include <mpi.h>
+#include <cstring>
 #include "input.h"
 #include "variable.h"
 #include "domain.h"
@@ -25,6 +23,7 @@
 #include "respa.h"
 #include "error.h"
 #include "force.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -101,6 +100,19 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
         estyle[nwall] = CONSTANT;
       }
 
+      if (utils::strmatch(style,"^wall/morse")) {
+        if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
+          int n = strlen(&arg[iarg+3][2]) + 1;
+          astr[nwall] = new char[n];
+          strcpy(astr[nwall],&arg[iarg+3][2]);
+          astyle[nwall] = VARIABLE;
+        } else {
+          alpha[nwall] = force->numeric(FLERR,arg[iarg+3]);
+          astyle[nwall] = CONSTANT;
+        }
+        ++iarg;
+      }
+
       if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
         int n = strlen(&arg[iarg+3][2]) + 1;
         sstr[nwall] = new char[n];
diff --git a/src/fix_wall.h b/src/fix_wall.h
index 82634c349f..b2bdc2e27c 100644
--- a/src/fix_wall.h
+++ b/src/fix_wall.h
@@ -45,12 +45,12 @@ class FixWall : public Fix {
   virtual void wall_particle(int, int, double) = 0;
 
  protected:
-  double epsilon[6],sigma[6],cutoff[6];
+  double epsilon[6],sigma[6],alpha[6],cutoff[6];
   double ewall[7],ewall_all[7];
   double xscale,yscale,zscale;
-  int estyle[6],sstyle[6],wstyle[6];
+  int estyle[6],sstyle[6],astyle[6],wstyle[6];
   int eindex[6],sindex[6];
-  char *estr[6],*sstr[6];
+  char *estr[6],*sstr[6],*astr[6];
   int varflag;                // 1 if any wall position,epsilon,sigma is a var
   int eflag;                  // per-wall flag for energy summation
   int ilevel_respa;
diff --git a/src/fix_wall_harmonic.cpp b/src/fix_wall_harmonic.cpp
index 4dc067178a..6c6d5ec402 100644
--- a/src/fix_wall_harmonic.cpp
+++ b/src/fix_wall_harmonic.cpp
@@ -11,7 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "fix_wall_harmonic.h"
 #include "atom.h"
 #include "error.h"
diff --git a/src/fix_wall_lj1043.cpp b/src/fix_wall_lj1043.cpp
index a93f4dd699..5656cf113d 100644
--- a/src/fix_wall_lj1043.cpp
+++ b/src/fix_wall_lj1043.cpp
@@ -15,8 +15,8 @@
    Contributing author: Jonathan Lee (Sandia)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "fix_wall_lj1043.h"
+#include <cmath>
 #include "atom.h"
 #include "math_const.h"
 
diff --git a/src/fix_wall_lj126.cpp b/src/fix_wall_lj126.cpp
index 369ef78c97..e748e2ef13 100644
--- a/src/fix_wall_lj126.cpp
+++ b/src/fix_wall_lj126.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "fix_wall_lj126.h"
+#include <cmath>
 #include "atom.h"
 #include "error.h"
 
diff --git a/src/fix_wall_lj93.cpp b/src/fix_wall_lj93.cpp
index ce5a06c81b..c0e81b60ee 100644
--- a/src/fix_wall_lj93.cpp
+++ b/src/fix_wall_lj93.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "fix_wall_lj93.h"
+#include <cmath>
 #include "atom.h"
 #include "error.h"
 
diff --git a/src/fix_wall_morse.cpp b/src/fix_wall_morse.cpp
new file mode 100644
index 0000000000..f854341e11
--- /dev/null
+++ b/src/fix_wall_morse.cpp
@@ -0,0 +1,87 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "fix_wall_morse.h"
+#include <cmath>
+#include "atom.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ---------------------------------------------------------------------- */
+
+FixWallMorse::FixWallMorse(LAMMPS *lmp, int narg, char **arg) :
+  FixWall(lmp, narg, arg)
+{
+  dynamic_group_allow = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixWallMorse::precompute(int m)
+{
+  coeff1[m] = 2.0 * epsilon[m] * alpha[m];
+  const double alpha_dr = -alpha[m] * (cutoff[m] - sigma[m]);
+  offset[m] = epsilon[m] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
+}
+
+/* ----------------------------------------------------------------------
+   interaction of all particles in group with a wall
+   m = index of wall coeffs
+   which = xlo,xhi,ylo,yhi,zlo,zhi
+   error if any particle is on or behind wall
+------------------------------------------------------------------------- */
+
+void FixWallMorse::wall_particle(int m, int which, double coord)
+{
+  double delta,fwall;
+  double vn;
+
+  double **x = atom->x;
+  double **f = atom->f;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  int dim = which / 2;
+  int side = which % 2;
+  if (side == 0) side = -1;
+
+  int onflag = 0;
+
+  for (int i = 0; i < nlocal; i++) {
+    if (mask[i] & groupbit) {
+      if (side < 0) delta = x[i][dim] - coord;
+      else delta = coord - x[i][dim];
+      if (delta >= cutoff[m]) continue;
+      if (delta <= 0.0) {
+        onflag = 1;
+        continue;
+      }
+      double dr = delta - sigma[m];
+      double dexp = exp(-alpha[m] * dr);
+      fwall = side * coeff1[m] * (dexp*dexp - dexp) / delta;
+      ewall[0] += epsilon[m] * (dexp*dexp - 2.0*dexp) - offset[m];
+      f[i][dim] -= fwall;
+      ewall[m+1] += fwall;
+
+      if (evflag) {
+        if (side < 0) vn = -fwall*delta;
+        else vn = fwall*delta;
+        v_tally(dim, i, vn);
+      }
+    }
+  }
+
+  if (onflag) error->one(FLERR,"Particle on or inside fix wall surface");
+}
diff --git a/src/fix_wall_morse.h b/src/fix_wall_morse.h
new file mode 100644
index 0000000000..a7359e9cde
--- /dev/null
+++ b/src/fix_wall_morse.h
@@ -0,0 +1,49 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(wall/morse,FixWallMorse)
+
+#else
+
+#ifndef LMP_FIX_WALL_MORSE_H
+#define LMP_FIX_WALL_MORSE_H
+
+#include "fix_wall.h"
+
+namespace LAMMPS_NS {
+
+class FixWallMorse : public FixWall {
+ public:
+  FixWallMorse(class LAMMPS *, int, char **);
+  void precompute(int);
+  void wall_particle(int, int, double);
+
+ private:
+  double coeff1[6],offset[6];
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Particle on or inside fix wall surface
+
+Particles must be "exterior" to the wall in order for energy/force to
+be calculated.
+
+*/
diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp
index 8acba72035..bc3414d650 100644
--- a/src/fix_wall_reflect.cpp
+++ b/src/fix_wall_reflect.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "fix_wall_reflect.h"
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "update.h"
diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp
index ff147d7446..70bde90d2b 100644
--- a/src/fix_wall_region.cpp
+++ b/src/fix_wall_region.cpp
@@ -11,18 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "fix_wall_region.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
 #include "domain.h"
 #include "region.h"
 #include "force.h"
-#include "lattice.h"
 #include "update.h"
-#include "output.h"
 #include "respa.h"
 #include "error.h"
 #include "math_const.h"
@@ -31,7 +28,7 @@ using namespace LAMMPS_NS;
 using namespace FixConst;
 using namespace MathConst;
 
-enum{LJ93,LJ126,LJ1043,COLLOID,HARMONIC};
+enum{LJ93,LJ126,LJ1043,COLLOID,HARMONIC,MORSE};
 
 /* ---------------------------------------------------------------------- */
 
@@ -39,7 +36,7 @@ FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
   idregion(NULL)
 {
-  if (narg != 8) error->all(FLERR,"Illegal fix wall/region command");
+  if (narg < 8) error->all(FLERR,"Illegal fix wall/region command");
 
   scalar_flag = 1;
   vector_flag = 1;
@@ -65,13 +62,28 @@ FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) :
   else if (strcmp(arg[4],"lj1043") == 0) style = LJ1043;
   else if (strcmp(arg[4],"colloid") == 0) style = COLLOID;
   else if (strcmp(arg[4],"harmonic") == 0) style = HARMONIC;
+  else if (strcmp(arg[4],"morse") == 0) style = MORSE;
   else error->all(FLERR,"Illegal fix wall/region command");
 
   if (style != COLLOID) dynamic_group_allow = 1;
 
-  epsilon = force->numeric(FLERR,arg[5]);
-  sigma = force->numeric(FLERR,arg[6]);
-  cutoff = force->numeric(FLERR,arg[7]);
+  if (style == MORSE) {
+    if (narg != 9)
+      error->all(FLERR,"Illegal fix wall/region command");
+
+    epsilon = force->numeric(FLERR,arg[5]);
+    alpha = force->numeric(FLERR,arg[6]);
+    sigma = force->numeric(FLERR,arg[7]);
+    cutoff = force->numeric(FLERR,arg[8]);
+
+  } else {
+    if (narg != 8)
+      error->all(FLERR,"Illegal fix wall/region command");
+
+    epsilon = force->numeric(FLERR,arg[5]);
+    sigma = force->numeric(FLERR,arg[6]);
+    cutoff = force->numeric(FLERR,arg[7]);
+  }
 
   if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region cutoff <= 0.0");
 
@@ -157,12 +169,15 @@ void FixWallRegion::init()
     coeff5 = coeff1 * 10.0;
     coeff6 = coeff2 * 4.0;
     coeff7 = coeff3 * 3.0;
-
     double rinv = 1.0/cutoff;
     double r2inv = rinv*rinv;
     double r4inv = r2inv*r2inv;
     offset = coeff1*r4inv*r4inv*r2inv - coeff2*r4inv -
       coeff3*pow(cutoff+coeff4,-3.0);
+  } else if (style == MORSE) {
+    coeff1 = 2 * epsilon * alpha;
+    double alpha_dr = -alpha * (cutoff - sigma);
+    offset = epsilon * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
   } else if (style == COLLOID) {
     coeff1 = -4.0/315.0 * epsilon * pow(sigma,6.0);
     coeff2 = -2.0/3.0 * epsilon;
@@ -253,6 +268,7 @@ void FixWallRegion::post_force(int vflag)
         if (style == LJ93) lj93(region->contact[m].r);
         else if (style == LJ126) lj126(region->contact[m].r);
         else if (style == LJ1043) lj1043(region->contact[m].r);
+        else if (style == MORSE) morse(region->contact[m].r);
         else if (style == COLLOID) colloid(region->contact[m].r,radius[i]);
         else harmonic(region->contact[m].r);
 
@@ -287,7 +303,7 @@ void FixWallRegion::post_force(int vflag)
 
 /* ---------------------------------------------------------------------- */
 
-void FixWallRegion::post_force_respa(int vflag, int ilevel, int /*iloop*/)
+void FixWallRegion::post_force_respa(int vflag, int ilevel, int /* iloop */)
 {
   if (ilevel == ilevel_respa) post_force(vflag);
 }
@@ -375,6 +391,19 @@ void FixWallRegion::lj1043(double r)
     coeff3*pow(r+coeff4,-3.0) - offset;
 }
 
+/* ----------------------------------------------------------------------
+   Morse interaction for particle with wall
+   compute eng and fwall = magnitude of wall force
+------------------------------------------------------------------------- */
+
+void FixWallRegion::morse(double r)
+{
+  double dr = r - sigma;
+  double dexp = exp(-alpha * dr);
+  fwall = coeff1 * (dexp*dexp - dexp) / r;
+  eng = epsilon * (dexp*dexp - 2.0*dexp) - offset;
+}
+
 /* ----------------------------------------------------------------------
    colloid interaction for finite-size particle of rad with wall
    compute eng and fwall = magnitude of wall force
diff --git a/src/fix_wall_region.h b/src/fix_wall_region.h
index e3688c99ee..663a12b257 100644
--- a/src/fix_wall_region.h
+++ b/src/fix_wall_region.h
@@ -41,6 +41,7 @@ class FixWallRegion : public Fix {
  private:
   int style,iregion;
   double epsilon,sigma,cutoff;
+  double alpha;
   int eflag;
   double ewall[4],ewall_all[4];
   int ilevel_respa;
@@ -53,6 +54,7 @@ class FixWallRegion : public Fix {
   void lj93(double);
   void lj126(double);
   void lj1043(double);
+  void morse(double);
   void colloid(double, double);
   void harmonic(double);
 };
diff --git a/src/force.cpp b/src/force.cpp
index 2648358932..1a826b2843 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -11,17 +11,16 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "force.h"
 #include <cstdlib>
 #include <cstring>
 #include <cctype>
-#include "force.h"
 #include "style_bond.h"
 #include "style_angle.h"
 #include "style_dihedral.h"
 #include "style_improper.h"
 #include "style_pair.h"
 #include "style_kspace.h"
-#include "atom.h"
 #include "comm.h"
 #include "pair.h"
 #include "pair_hybrid.h"
@@ -32,8 +31,6 @@
 #include "dihedral.h"
 #include "improper.h"
 #include "kspace.h"
-#include "group.h"
-#include "memory.h"
 #include "error.h"
 #include "utils.h"
 
diff --git a/src/force.h b/src/force.h
index 227b9427c0..26a3ecdfb8 100644
--- a/src/force.h
+++ b/src/force.h
@@ -15,7 +15,6 @@
 #define LMP_FORCE_H
 
 #include "pointers.h"
-#include <cstdio>
 #include <map>
 #include <string>
 
diff --git a/src/group.cpp b/src/group.cpp
index 256bab7778..d119964ea1 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -11,12 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "group.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstring>
-#include <cstdlib>
-#include "group.h"
+#include <utility>
 #include "domain.h"
 #include "atom.h"
 #include "force.h"
diff --git a/src/group.h b/src/group.h
index 962d37b32a..ec913f98bc 100644
--- a/src/group.h
+++ b/src/group.h
@@ -14,7 +14,6 @@
 #ifndef LMP_GROUP_H
 #define LMP_GROUP_H
 
-#include <cstdio>
 #include "pointers.h"
 #include <map>
 
diff --git a/src/hashlittle.cpp b/src/hashlittle.cpp
index f612be9eeb..c3824b71fe 100644
--- a/src/hashlittle.cpp
+++ b/src/hashlittle.cpp
@@ -2,9 +2,7 @@
 // from lookup3.c, by Bob Jenkins, May 2006, Public Domain
 // bob_jenkins@burtleburtle.net
 
-#include <cmath>
-#include <stddef.h>
-#include <stdint.h>
+#include "hashlittle.h"
 
 // if the system defines the __BYTE_ORDER__ define,
 // we use it instead of guessing the platform
@@ -142,7 +140,7 @@ acceptable.  Do NOT use for cryptographic purposes.
 -------------------------------------------------------------------------------
 */
 
-uint32_t hashlittle( const void *key, size_t length, uint32_t initval)
+uint32_t LAMMPS_NS::hashlittle(const void *key, size_t length, uint32_t initval)
 {
 #ifndef PURIFY_HATES_HASHLITTLE
 
diff --git a/src/hashlittle.h b/src/hashlittle.h
index 7b57a35c80..75380d366b 100644
--- a/src/hashlittle.h
+++ b/src/hashlittle.h
@@ -2,4 +2,13 @@
 // from lookup3.c, by Bob Jenkins, May 2006, Public Domain
 // bob_jenkins@burtleburtle.net
 
-uint32_t hashlittle(const void *key, size_t length, uint32_t);
+#ifndef LMP_HASHLITTLE_H
+#define LMP_HASHLITTLE_H
+
+#include <cstddef>
+#include <stdint.h>
+
+namespace LAMMPS_NS {
+  uint32_t hashlittle(const void *key, size_t length, uint32_t);
+}
+#endif
diff --git a/src/image.cpp b/src/image.cpp
index 3df167bbf6..4a5009b8ed 100644
--- a/src/image.cpp
+++ b/src/image.cpp
@@ -15,12 +15,11 @@
    Contributing author: Nathan Fabian (Sandia)
 ------------------------------------------------------------------------- */
 
+#include "image.h"
 #include <mpi.h>
 #include <cmath>
 #include <cctype>
-#include <cstdlib>
 #include <cstring>
-#include "image.h"
 #include "math_extra.h"
 #include "random_mars.h"
 #include "math_const.h"
@@ -29,7 +28,7 @@
 #include "memory.h"
 
 #ifdef LAMMPS_JPEG
-#include "jpeglib.h"
+#include <jpeglib.h>
 #endif
 
 #ifdef LAMMPS_PNG
diff --git a/src/image.h b/src/image.h
index 5672bf85c5..7df81425d9 100644
--- a/src/image.h
+++ b/src/image.h
@@ -15,7 +15,6 @@
 #define LMP_IMAGE_H
 
 #include <cmath>
-#include <cstdio>
 #include "pointers.h"
 
 namespace LAMMPS_NS {
diff --git a/src/imbalance.h b/src/imbalance.h
index d3c3b9a642..0cc4ac844e 100644
--- a/src/imbalance.h
+++ b/src/imbalance.h
@@ -14,8 +14,7 @@
 #ifndef LMP_IMBALANCE_H
 #define LMP_IMBALANCE_H
 
-#include <cstdio>
-#include "pointers.h"
+#include "pointers.h"  // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
diff --git a/src/imbalance_neigh.cpp b/src/imbalance_neigh.cpp
index 2a55754da8..19f3915a11 100644
--- a/src/imbalance_neigh.cpp
+++ b/src/imbalance_neigh.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "imbalance_neigh.h"
+#include <mpi.h>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp
index 6b69caf785..343d47b189 100644
--- a/src/imbalance_store.cpp
+++ b/src/imbalance_store.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "imbalance_store.h"
+#include <cstring>
 #include "atom.h"
-#include "input.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/imbalance_time.cpp b/src/imbalance_time.cpp
index a5fe538b8f..0831713204 100644
--- a/src/imbalance_time.cpp
+++ b/src/imbalance_time.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "imbalance_time.h"
+#include <mpi.h>
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
 #include "timer.h"
 #include "error.h"
diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp
index e089b1df0c..ba84ef01ef 100644
--- a/src/imbalance_var.cpp
+++ b/src/imbalance_var.cpp
@@ -11,8 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "imbalance_var.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "group.h"
 #include "input.h"
@@ -20,9 +21,6 @@
 #include "memory.h"
 #include "error.h"
 
-// DEBUG
-#include "update.h"
-
 using namespace LAMMPS_NS;
 
 /* -------------------------------------------------------------------- */
diff --git a/src/improper.cpp b/src/improper.cpp
index 17e2df4e59..eefe3222ee 100644
--- a/src/improper.cpp
+++ b/src/improper.cpp
@@ -11,7 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "improper.h"
 #include "atom.h"
 #include "comm.h"
diff --git a/src/improper.h b/src/improper.h
index 876c928d7e..c30079bb5e 100644
--- a/src/improper.h
+++ b/src/improper.h
@@ -14,8 +14,7 @@
 #ifndef LMP_IMPROPER_H
 #define LMP_IMPROPER_H
 
-#include <cstdio>
-#include "pointers.h"
+#include "pointers.h"  // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
diff --git a/src/improper_deprecated.cpp b/src/improper_deprecated.cpp
index 6f4d08764f..62a688527a 100644
--- a/src/improper_deprecated.cpp
+++ b/src/improper_deprecated.cpp
@@ -15,8 +15,8 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "improper_deprecated.h"
+#include <cstring>
 #include "improper_hybrid.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp
index 174f54907e..730a75766c 100644
--- a/src/improper_hybrid.cpp
+++ b/src/improper_hybrid.cpp
@@ -11,13 +11,12 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
+#include "improper_hybrid.h"
+#include <mpi.h>
 #include <cstring>
 #include <cctype>
-#include "improper_hybrid.h"
 #include "atom.h"
 #include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "memory.h"
diff --git a/src/improper_hybrid.h b/src/improper_hybrid.h
index 89595ccfc4..3e5423b173 100644
--- a/src/improper_hybrid.h
+++ b/src/improper_hybrid.h
@@ -20,7 +20,6 @@ ImproperStyle(hybrid,ImproperHybrid)
 #ifndef LMP_IMPROPER_HYBRID_H
 #define LMP_IMPROPER_HYBRID_H
 
-#include <cstdio>
 #include "improper.h"
 
 namespace LAMMPS_NS {
diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp
index 747dd57919..efa70c8ff5 100644
--- a/src/improper_zero.cpp
+++ b/src/improper_zero.cpp
@@ -15,13 +15,10 @@
    Contributing author: Carsten Svaneborg (SDU)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "improper_zero.h"
+#include <cstring>
 #include "atom.h"
 #include "force.h"
-#include "comm.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/improper_zero.h b/src/improper_zero.h
index 0a2290b6f7..1a70059070 100644
--- a/src/improper_zero.h
+++ b/src/improper_zero.h
@@ -20,7 +20,6 @@ ImproperStyle(zero,ImproperZero)
 #ifndef LMP_IMPROPER_ZERO_H
 #define LMP_IMPROPER_ZERO_H
 
-#include <cstdio>
 #include "improper.h"
 
 namespace LAMMPS_NS {
diff --git a/src/info.cpp b/src/info.cpp
index 25b9879408..caa2d6fdd0 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -16,8 +16,14 @@
                           Richard Berger (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "info.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <cctype>
+#include <ctime>
+#include <map>
+#include <string>
 #include "accelerator_kokkos.h"
 #include "atom.h"
 #include "comm.h"
@@ -44,23 +50,17 @@
 #include "error.h"
 #include "utils.h"
 
-#include <ctime>
-#include <map>
-#include <string>
-#include <algorithm>
-
 #ifdef _WIN32
 #define PSAPI_VERSION 1
 #include <windows.h>
 #include <stdint.h> // <cstdint> requires C++-11
 #include <psapi.h>
 #else
-#include <sys/time.h>
 #include <sys/resource.h>
 #include <sys/utsname.h>
 #endif
 
-#if defined __linux
+#if defined(__linux)
 #include <malloc.h>
 #endif
 
@@ -353,11 +353,24 @@ void Info::command(int narg, char **arg)
   }
 
   if (flags & COMM) {
-    int major,minor;
+    int major,minor,len;
+#if (defined(MPI_VERSION) && (MPI_VERSION > 2)) || defined(MPI_STUBS)
+    char version[MPI_MAX_LIBRARY_VERSION_STRING];
+    MPI_Get_library_version(version,&len);
+#else
+    char version[] = "Undetected MPI implementation";
+    len = strlen(version);
+#endif
+
     MPI_Get_version(&major,&minor);
+    if (len > 80) {
+      char *ptr = strchr(version+80,'\n');
+      if (ptr) *ptr = '\0';
+    }
 
     fprintf(out,"\nCommunication information:\n");
     fprintf(out,"MPI library level: MPI v%d.%d\n",major,minor);
+    fprintf(out,"MPI version: %s\n",version);
     fprintf(out,"Comm style = %s,  Comm layout = %s\n",
             commstyles[comm->style], commlayout[comm->layout]);
     fprintf(out,"Communicate velocities for ghost atoms = %s\n",
@@ -366,7 +379,7 @@ void Info::command(int narg, char **arg)
     if (comm->mode == 0) {
       fprintf(out,"Communication mode = single\n");
       fprintf(out,"Communication cutoff = %g\n",
-              MAX(comm->cutghostuser,neighbor->cutneighmax));
+              comm->get_comm_cutoff());
     }
 
     if (comm->mode == 1) {
diff --git a/src/input.cpp b/src/input.cpp
index 08e3655437..6adf37e847 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -11,15 +11,14 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "input.h"
 #include <mpi.h>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 #include <errno.h>
 #include <cctype>
 #include <unistd.h>
 #include <sys/stat.h>
-#include "input.h"
 #include "style_command.h"
 #include "universe.h"
 #include "atom.h"
@@ -52,10 +51,6 @@
 #include "memory.h"
 #include "utils.h"
 
-#ifdef _OPENMP
-#include <omp.h>
-#endif
-
 #ifdef _WIN32
 #include <direct.h>
 #endif
@@ -314,6 +309,17 @@ char *Input::one(const char *single)
   return command;
 }
 
+/* ----------------------------------------------------------------------
+   Send text to active echo file pointers
+------------------------------------------------------------------------- */
+void Input::write_echo(const char *txt)
+{
+  if (me == 0) {
+    if (echo_screen && screen) fputs(txt,screen);
+    if (echo_log && logfile) fputs(txt,logfile);
+  }
+}
+
 /* ----------------------------------------------------------------------
    parse copy of command line by inserting string terminators
    strip comment = all chars from # on
@@ -1666,7 +1672,7 @@ void Input::min_style()
 {
   if (domain->box_exist == 0)
     error->all(FLERR,"Min_style command before simulation box is defined");
-  update->create_minimize(narg,arg);
+  update->create_minimize(narg,arg,1);
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/input.h b/src/input.h
index 7b6e55c2ba..4b274c17a9 100644
--- a/src/input.h
+++ b/src/input.h
@@ -14,7 +14,6 @@
 #ifndef LMP_INPUT_H
 #define LMP_INPUT_H
 
-#include <cstdio>
 #include "pointers.h"
 #include <map>
 #include <string>
@@ -39,17 +38,18 @@ class Input : protected Pointers {
   void substitute(char *&, char *&, int &, int &, int);
                                  // substitute for variables in a string
   int expand_args(int, char **, int, char **&);  // expand args due to wildcard
-
+  void write_echo(const char *); // send text to active echo file pointers
+  
  protected:
   char *command;               // ptr to current command
+  int echo_screen;             // 0 = no, 1 = yes
+  int echo_log;                // 0 = no, 1 = yes
 
  private:
   int me;                      // proc ID
   int maxarg;                  // max # of args in arg
   char *line,*copy,*work;      // input line & copy and work string
   int maxline,maxcopy,maxwork; // max lengths of char strings
-  int echo_screen;             // 0 = no, 1 = yes
-  int echo_log;                // 0 = no, 1 = yes
   int nfile,maxfile;           // current # and max # of open input files
   int label_active;            // 0 = no label, 1 = looking for label
   char *labelstr;              // label string being looked for
diff --git a/src/integrate.cpp b/src/integrate.cpp
index d6b27e042d..545de849d5 100644
--- a/src/integrate.cpp
+++ b/src/integrate.cpp
@@ -11,7 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "integrate.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/irregular.cpp b/src/irregular.cpp
index 1865f9cbf6..2213b37d55 100644
--- a/src/irregular.cpp
+++ b/src/irregular.cpp
@@ -11,14 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdlib>
-#include <cstring>
 #include "irregular.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "domain.h"
 #include "comm.h"
+#include "modify.h"
+#include "fix.h"
 #include "memory.h"
 
 using namespace LAMMPS_NS;
@@ -35,8 +36,8 @@ static int compare_standalone(const int, const int, void *);
 #endif
 
 #define BUFFACTOR 1.5
-#define BUFMIN 1000
-#define BUFEXTRA 1000
+#define BUFMIN 1024
+#define BUFEXTRA 1024
 
 /* ---------------------------------------------------------------------- */
 
@@ -69,9 +70,10 @@ Irregular::Irregular(LAMMPS *lmp) : Pointers(lmp)
   // initialize buffers for migrate atoms, not used for datum comm
   // these can persist for multiple irregular operations
 
-  maxsend = BUFMIN;
-  memory->create(buf_send,maxsend+BUFEXTRA,"comm:buf_send");
-  maxrecv = BUFMIN;
+  buf_send = buf_recv = NULL;
+  maxsend = maxrecv = BUFMIN;
+  bufextra = BUFEXTRA;
+  grow_send(maxsend,2);
   memory->create(buf_recv,maxrecv,"comm:buf_recv");
 }
 
@@ -103,6 +105,13 @@ Irregular::~Irregular()
 
 void Irregular::migrate_atoms(int sortflag, int preassign, int *procassign)
 {
+  // check if buf_send needs to be extended due to atom style or per-atom fixes
+  // same as in Comm::exchange()
+
+  int bufextra_old = bufextra;
+  init_exchange();
+  if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
+
   // clear global->local map since atoms move to new procs
   // clear old ghosts so map_set() at end will operate only on local atoms
   // exchange() doesn't need to clear ghosts b/c borders()
@@ -983,24 +992,52 @@ void Irregular::destroy_data()
 }
 
 /* ----------------------------------------------------------------------
-   realloc the size of the send buffer as needed with BUFFACTOR & BUFEXTRA
-   if flag = 1, realloc
-   if flag = 0, don't need to realloc with copy, just free/malloc
+   set bufextra based on AtomVec and fixes
+   similar to Comm::init_exchange()
+------------------------------------------------------------------------- */
+
+void Irregular::init_exchange()
+{
+  int nfix = modify->nfix;
+  Fix **fix = modify->fix;
+
+  int onefix;
+  int maxexchange_fix = 0;
+  for (int i = 0; i < nfix; i++) {
+    onefix = fix[i]->maxexchange;
+    maxexchange_fix = MAX(maxexchange_fix,onefix);
+  }
+
+  int maxexchange = atom->avec->maxexchange + maxexchange_fix;
+  bufextra = maxexchange + BUFEXTRA;
+}
+
+/* ----------------------------------------------------------------------
+   realloc the size of the send buffer as needed with BUFFACTOR and bufextra
+   flag = 0, don't need to realloc with copy, just free/malloc w/ BUFFACTOR
+   flag = 1, realloc with BUFFACTOR
+   flag = 2, free/malloc w/out BUFFACTOR
+   same as Comm::grow_send()
 ------------------------------------------------------------------------- */
 
 void Irregular::grow_send(int n, int flag)
 {
-  maxsend = static_cast<int> (BUFFACTOR * n);
-  if (flag)
-    memory->grow(buf_send,maxsend+BUFEXTRA,"comm:buf_send");
-  else {
+  if (flag == 0) {
+    maxsend = static_cast<int> (BUFFACTOR * n);
     memory->destroy(buf_send);
-    memory->create(buf_send,maxsend+BUFEXTRA,"comm:buf_send");
+    memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
+  } else if (flag == 1) {
+    maxsend = static_cast<int> (BUFFACTOR * n);
+    memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
+  } else {
+    memory->destroy(buf_send);
+    memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
   }
 }
 
 /* ----------------------------------------------------------------------
    free/malloc the size of the recv buffer as needed with BUFFACTOR
+   same as Comm::grow_recv()
 ------------------------------------------------------------------------- */
 
 void Irregular::grow_recv(int n)
diff --git a/src/irregular.h b/src/irregular.h
index d56bcb253d..01fe40c46b 100644
--- a/src/irregular.h
+++ b/src/irregular.h
@@ -43,6 +43,7 @@ class Irregular : protected Pointers {
   int triclinic;
   int map_style;
 
+  int bufextra;                     // augment send buf size for a migrating atom
   int maxsend,maxrecv;              // size of buf send/recv in # of doubles
   double *buf_send,*buf_recv;       // bufs used in migrate_atoms
   int maxdbuf;                      // size of double buf in bytes
@@ -91,6 +92,7 @@ class Irregular : protected Pointers {
 
   int binary(double, int, double *);
 
+  void init_exchange();             // reset bufxtra
   void grow_send(int,int);          // reallocate send buffer
   void grow_recv(int);              // free/allocate recv buffer
 };
diff --git a/src/kspace.cpp b/src/kspace.cpp
index 643cf22113..f9020416bf 100644
--- a/src/kspace.cpp
+++ b/src/kspace.cpp
@@ -11,9 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "kspace.h"
+#include <mpi.h>
+#include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "kspace.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/kspace.h b/src/kspace.h
index 69f4ccb433..c04a0db989 100644
--- a/src/kspace.h
+++ b/src/kspace.h
@@ -14,7 +14,7 @@
 #ifndef LMP_KSPACE_H
 #define LMP_KSPACE_H
 
-#include "pointers.h"
+#include "pointers.h"  // IWYU pragma: export
 
 #ifdef FFT_SINGLE
 typedef float FFT_SCALAR;
diff --git a/src/kspace_deprecated.cpp b/src/kspace_deprecated.cpp
index 1d62de2692..0b6490b4cf 100644
--- a/src/kspace_deprecated.cpp
+++ b/src/kspace_deprecated.cpp
@@ -15,8 +15,8 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "kspace_deprecated.h"
+#include <cstring>
 #include "comm.h"
 #include "force.h"
 #include "error.h"
diff --git a/src/lammps.cpp b/src/lammps.cpp
index f8d04c9323..5ddc1600a4 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -11,26 +11,28 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "lammps.h"
 #include <mpi.h>
+#include <cmath>
 #include <cstring>
+#include <cstdlib>
 #include <cctype>
 #include <map>
 #include <string>
-#include "lammps.h"
-#include "style_angle.h"
-#include "style_atom.h"
-#include "style_bond.h"
-#include "style_command.h"
-#include "style_compute.h"
-#include "style_dihedral.h"
-#include "style_dump.h"
-#include "style_fix.h"
-#include "style_improper.h"
-#include "style_integrate.h"
-#include "style_kspace.h"
-#include "style_minimize.h"
-#include "style_pair.h"
-#include "style_region.h"
+#include "style_angle.h"     // IWYU pragma: keep
+#include "style_atom.h"      // IWYU pragma: keep
+#include "style_bond.h"      // IWYU pragma: keep
+#include "style_command.h"   // IWYU pragma: keep
+#include "style_compute.h"   // IWYU pragma: keep
+#include "style_dihedral.h"  // IWYU pragma: keep
+#include "style_dump.h"      // IWYU pragma: keep
+#include "style_fix.h"       // IWYU pragma: keep
+#include "style_improper.h"  // IWYU pragma: keep
+#include "style_integrate.h" // IWYU pragma: keep
+#include "style_kspace.h"    // IWYU pragma: keep
+#include "style_minimize.h"  // IWYU pragma: keep
+#include "style_pair.h"      // IWYU pragma: keep
+#include "style_region.h"    // IWYU pragma: keep
 #include "universe.h"
 #include "input.h"
 #include "info.h"
@@ -46,7 +48,7 @@
 #include "output.h"
 #include "citeme.h"
 #include "accelerator_kokkos.h"
-#include "accelerator_omp.h"
+#include "accelerator_omp.h"    // IWYU pragma: keep
 #include "timer.h"
 #include "lmppython.h"
 #include "version.h"
diff --git a/src/lammps.h b/src/lammps.h
index e02d0c764a..dc2916f214 100644
--- a/src/lammps.h
+++ b/src/lammps.h
@@ -14,6 +14,7 @@
 #ifndef LMP_LAMMPS_H
 #define LMP_LAMMPS_H
 
+#include <mpi.h>
 #include <cstdio>
 
 namespace LAMMPS_NS {
diff --git a/src/lattice.cpp b/src/lattice.cpp
index ee2fea2a75..98faf680e8 100644
--- a/src/lattice.cpp
+++ b/src/lattice.cpp
@@ -11,10 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "lattice.h"
 #include <cmath>
 #include <cstring>
 #include <cstdlib>
-#include "lattice.h"
 #include "update.h"
 #include "domain.h"
 #include "comm.h"
diff --git a/src/library.cpp b/src/library.cpp
index a653b83adb..6f283ea4da 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -14,14 +14,12 @@
 // C or Fortran style library interface to LAMMPS
 // customize by adding new LAMMPS-specific functions
 
+#include "library.h"
 #include <mpi.h>
+#include <cctype>
 #include <cstring>
 #include <cstdlib>
-#include "library.h"
-#include "lmptype.h"
-#include "lammps.h"
 #include "universe.h"
-#include "input.h"
 #include "atom_vec.h"
 #include "atom.h"
 #include "domain.h"
@@ -39,6 +37,11 @@
 #include "error.h"
 #include "force.h"
 #include "info.h"
+#include "fix_external.h"
+
+#if defined(LAMMPS_EXCEPTIONS)
+#include "exceptions.h"
+#endif
 
 using namespace LAMMPS_NS;
 
@@ -808,7 +811,10 @@ void lammps_gather_atoms(void *ptr, char * /*name */,
   LAMMPS *lmp = (LAMMPS *) ptr;
 
   BEGIN_CAPTURE
-  lmp->error->all(FLERR,"Library function lammps_gather_atoms() not compatible with -DLAMMPS_BIGBIG");
+  {
+    lmp->error->all(FLERR,"Library function lammps_gather_atoms() "
+                    "is not compatible with -DLAMMPS_BIGBIG");
+  }
   END_CAPTURE
 }
 #else
@@ -946,7 +952,10 @@ void lammps_gather_atoms_concat(void *ptr, char * /*name */,
   LAMMPS *lmp = (LAMMPS *) ptr;
 
   BEGIN_CAPTURE
-  lmp->error->all(FLERR,"Library function lammps_gather_atoms_concat() not compatible with -DLAMMPS_BIGBIG");
+  {
+    lmp->error->all(FLERR,"Library function lammps_gather_atoms_concat() "
+                    "is not compatible with -DLAMMPS_BIGBIG");
+  }
   END_CAPTURE
 }
 #else
@@ -1103,7 +1112,10 @@ void lammps_gather_atoms_subset(void *ptr, char * /*name */,
   LAMMPS *lmp = (LAMMPS *) ptr;
 
   BEGIN_CAPTURE
-  lmp->error->all(FLERR,"Library function lammps_gather_atoms_subset() not compatible with -DLAMMPS_BIGBIG");
+  {
+    lmp->error->all(FLERR,"Library function lammps_gather_atoms_subset() "
+                    "is not compatible with -DLAMMPS_BIGBIG");
+  }
   END_CAPTURE
 }
 #else
@@ -1249,7 +1261,10 @@ void lammps_scatter_atoms(void *ptr, char * /*name */,
   LAMMPS *lmp = (LAMMPS *) ptr;
 
   BEGIN_CAPTURE
-  lmp->error->all(FLERR,"Library function lammps_scatter_atoms() not compatible with -DLAMMPS_BIGBIG");
+  {
+    lmp->error->all(FLERR,"Library function lammps_scatter_atoms() "
+                    "is not compatible with -DLAMMPS_BIGBIG");
+  }
   END_CAPTURE
 }
 #else
@@ -1375,7 +1390,10 @@ void lammps_scatter_atoms_subset(void *ptr, char * /*name */,
   LAMMPS *lmp = (LAMMPS *) ptr;
 
   BEGIN_CAPTURE
-  lmp->error->all(FLERR,"Library function lammps_scatter_atoms_subset() not compatible with -DLAMMPS_BIGBIG");
+  {
+    lmp->error->all(FLERR,"Library function lammps_scatter_atoms_subset() "
+                    "is not compatible with -DLAMMPS_BIGBIG");
+  }
   END_CAPTURE
 }
 #else
@@ -1578,7 +1596,7 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
 
     if (lmp->atom->natoms != natoms_prev + n) {
       char str[128];
-      sprintf(str,"Library warning in lammps_create_atoms, "
+      snprintf(str, 128, "Library warning in lammps_create_atoms, "
               "invalid total atoms " BIGINT_FORMAT " " BIGINT_FORMAT,
               lmp->atom->natoms,natoms_prev+n);
       if (lmp->comm->me == 0)
@@ -1588,6 +1606,40 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
   END_CAPTURE
 }
 
+/* ----------------------------------------------------------------------
+   find fix external with given ID and set the callback function
+   and caller pointer
+------------------------------------------------------------------------- */
+
+void lammps_set_fix_external_callback(void *ptr, char *id, FixExternalFnPtr callback_ptr, void * caller)
+{
+  LAMMPS *lmp = (LAMMPS *) ptr;
+  FixExternal::FnPtr callback = (FixExternal::FnPtr) callback_ptr;
+
+  BEGIN_CAPTURE
+  {
+    int ifix = lmp->modify->find_fix(id);
+    if (ifix < 0) {
+      char str[128];
+      snprintf(str, 128, "Can not find fix with ID '%s'!", id);
+      lmp->error->all(FLERR,str);
+    }
+
+    Fix *fix = lmp->modify->fix[ifix];
+
+    if (strcmp("external",fix->style) != 0){
+      char str[128];
+      snprintf(str, 128, "Fix '%s' is not of style external!", id);
+      lmp->error->all(FLERR,str);
+    }
+
+    FixExternal * fext = (FixExternal*) fix;
+    fext->set_callback(callback, caller);
+  }
+  END_CAPTURE
+}
+
+
 // ----------------------------------------------------------------------
 // library API functions for accessing LAMMPS configuration
 // ----------------------------------------------------------------------
diff --git a/src/library.h b/src/library.h
index f6f8d9d75c..59b68b9502 100644
--- a/src/library.h
+++ b/src/library.h
@@ -17,7 +17,9 @@
 */
 
 #include <mpi.h>
+#ifdef LAMMPS_BIGBIG
 #include <inttypes.h>  /* for int64_t */
+#endif
 
 /* ifdefs allow this file to be included in a C program */
 
@@ -56,6 +58,14 @@ void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *);
 void lammps_scatter_atoms(void *, char *, int, int, void *);
 void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *);
 
+#ifdef LAMMPS_BIGBIG
+typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
+void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
+#else
+typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);
+void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
+#endif
+
 int lammps_config_has_package(char * package_name);
 int lammps_config_package_count();
 int lammps_config_package_name(int index, char * buffer, int max_size);
diff --git a/src/lmppython.cpp b/src/lmppython.cpp
index 7c6a490c24..52abd93f10 100644
--- a/src/lmppython.cpp
+++ b/src/lmppython.cpp
@@ -12,7 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "lmppython.h"
+#if LMP_PYTHON
+#include "python_impl.h"
+#else
 #include "error.h"
+#endif
 
 using namespace LAMMPS_NS;
 
diff --git a/src/lmppython.h b/src/lmppython.h
index afc21037fb..3d55c4827b 100644
--- a/src/lmppython.h
+++ b/src/lmppython.h
@@ -51,11 +51,6 @@ private:
 };
 
 }
-
-#endif
-
-#if LMP_PYTHON
-#include "python_impl.h"
 #endif
 
 /* ERROR/WARNING messages:
diff --git a/src/lmptype.h b/src/lmptype.h
index 12fa6cc4fb..65e46535fc 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -37,6 +37,7 @@
 #endif
 
 #include <climits>
+#include <cstdlib>
 #include <stdint.h>   // <cstdint> requires C++-11
 #include <inttypes.h> // <cinttypes> requires C++-11
 
@@ -48,10 +49,6 @@
 
 namespace LAMMPS_NS {
 
-// enum used for KOKKOS host/device flags
-
-enum ExecutionSpace{Host,Device};
-
 // reserve 2 hi bits in molecular system neigh list for special bonds flag
 // max local + ghost atoms per processor = 2^30 - 1
 
diff --git a/src/main.cpp b/src/main.cpp
index 8eb5e4e543..85e25aa2e4 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -11,12 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "lammps.h"
+#include <mpi.h>
 #include "input.h"
-#include "error.h"
-#include <cstdio>
-#include <cstdlib>
 
 #if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE)
 #include <fenv.h>
@@ -26,6 +23,10 @@
 #include <fftw3.h>
 #endif
 
+#if defined(LAMMPS_EXCEPTIONS)
+#include "exceptions.h"
+#endif
+
 using namespace LAMMPS_NS;
 
 /* ----------------------------------------------------------------------
diff --git a/src/math_extra.cpp b/src/math_extra.cpp
index f7e5bb646b..797d210d0e 100644
--- a/src/math_extra.cpp
+++ b/src/math_extra.cpp
@@ -15,9 +15,9 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
+#include "math_extra.h"
 #include <cstdio>
 #include <cstring>
-#include "math_extra.h"
 
 #define MAXJACOBI 50
 
diff --git a/src/math_extra.h b/src/math_extra.h
index 85f57224cf..09b135c641 100644
--- a/src/math_extra.h
+++ b/src/math_extra.h
@@ -19,9 +19,6 @@
 #define LMP_MATH_EXTRA_H
 
 #include <cmath>
-#include <cstdio>
-#include <cstring>
-#include "error.h"
 
 namespace MathExtra {
 
diff --git a/src/math_special.cpp b/src/math_special.cpp
index 31567bdc77..bf11a1ad45 100644
--- a/src/math_special.cpp
+++ b/src/math_special.cpp
@@ -1,6 +1,6 @@
-#include <cmath>
-#include <stdint.h> // <cstdint> requires C++-11
 #include "math_special.h"
+#include <cmath>
+#include <stdint.h> // IWYU pragma: keep
 
 using namespace LAMMPS_NS;
 
diff --git a/src/memory.cpp b/src/memory.cpp
index b2f8a95b17..a513dde6c2 100644
--- a/src/memory.cpp
+++ b/src/memory.cpp
@@ -11,10 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "memory.h"
+#include <cstdlib>
 #include "error.h"
 
 #if defined(LMP_USER_INTEL) && defined(__INTEL_COMPILER)
diff --git a/src/memory.h b/src/memory.h
index c5eddc7fe7..42c9bf6aba 100644
--- a/src/memory.h
+++ b/src/memory.h
@@ -14,7 +14,6 @@
 #ifndef LMP_MEMORY_H
 #define LMP_MEMORY_H
 
-#include "lmptype.h"
 #include "pointers.h"
 
 namespace LAMMPS_NS {
diff --git a/src/min.cpp b/src/min.cpp
index 2a42a444a0..b6bed01c75 100644
--- a/src/min.cpp
+++ b/src/min.cpp
@@ -19,10 +19,10 @@
             JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "min.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "domain.h"
@@ -68,6 +68,8 @@ Min::Min(LAMMPS *lmp) : Pointers(lmp)
   requestor = NULL;
 
   external_force_clear = 0;
+
+  kokkosable = 0;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -93,6 +95,10 @@ Min::~Min()
 
 void Min::init()
 {
+  if (lmp->kokkos && !kokkosable)
+    error->all(FLERR,"Must use a Kokkos-enabled min style (e.g. min_style cg/kk) "
+     "with Kokkos minimize");
+
   // create fix needed for storing atom-based quantities
   // will delete it at end of run
 
diff --git a/src/min.h b/src/min.h
index a63254231c..835e6b3ed5 100644
--- a/src/min.h
+++ b/src/min.h
@@ -31,16 +31,16 @@ class Min : protected Pointers {
   Min(class LAMMPS *);
   virtual ~Min();
   virtual void init();
-  void setup(int flag=1);
-  void setup_minimal(int);
-  void run(int);
+  virtual void setup(int flag=1);
+  virtual void setup_minimal(int);
+  virtual void run(int);
   void cleanup();
   int request(class Pair *, int, double);
   virtual bigint memory_usage() {return 0;}
   void modify_params(int, char **);
   virtual int modify_param(int, char **) {return 0;}
-  double fnorm_sqr();
-  double fnorm_inf();
+  virtual double fnorm_sqr();
+  virtual double fnorm_inf();
 
   virtual void init_style() {}
   virtual void setup_style() = 0;
@@ -97,10 +97,12 @@ class Min : protected Pointers {
   double *extra_max;          // max allowed change per iter for atom's var
   class Pair **requestor;     // Pair that stores/manipulates the variable
 
+  int kokkosable;             // 1 if this min style supports Kokkos
+
   int neigh_every,neigh_delay,neigh_dist_check;  // neighboring params
 
-  double energy_force(int);
-  void force_clear();
+  virtual double energy_force(int);
+  virtual void force_clear();
 
   double compute_force_norm_sqr();
   double compute_force_norm_inf();
diff --git a/src/min_cg.cpp b/src/min_cg.cpp
index 20e8cc30dd..ff318d23da 100644
--- a/src/min_cg.cpp
+++ b/src/min_cg.cpp
@@ -11,11 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "min_cg.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstring>
-#include "min_cg.h"
-#include "atom.h"
 #include "update.h"
 #include "output.h"
 #include "timer.h"
diff --git a/src/min_fire.cpp b/src/min_fire.cpp
index a50071d562..b7f853afd2 100644
--- a/src/min_fire.cpp
+++ b/src/min_fire.cpp
@@ -11,15 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "min_fire.h"
+#include <mpi.h>
+#include <cmath>
 #include "universe.h"
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "output.h"
 #include "timer.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp
index 0c834fbeb4..dcfed10fef 100644
--- a/src/min_hftn.cpp
+++ b/src/min_hftn.cpp
@@ -17,11 +17,12 @@
             "Parallel Unconstrained Min", Plantenga, SAND98-8201
 ------------------------------------------------------------------------- */
 
+#include "min_hftn.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstring>
 #include "atom.h"
 #include "fix_minimize.h"
-#include "min_hftn.h"
 #include "modify.h"
 #include "output.h"
 #include "pair.h"
diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp
index f93a56b09d..a7a10dcd51 100644
--- a/src/min_linesearch.cpp
+++ b/src/min_linesearch.cpp
@@ -21,19 +21,15 @@
             JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "min_linesearch.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
-#include "update.h"
-#include "neighbor.h"
-#include "domain.h"
 #include "modify.h"
 #include "fix_minimize.h"
 #include "pair.h"
 #include "output.h"
 #include "thermo.h"
-#include "timer.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp
index 8b48816355..04e72b046d 100644
--- a/src/min_quickmin.cpp
+++ b/src/min_quickmin.cpp
@@ -11,16 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "min_quickmin.h"
 #include <mpi.h>
 #include <cmath>
-#include "min_quickmin.h"
 #include "universe.h"
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "output.h"
 #include "timer.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/min_sd.cpp b/src/min_sd.cpp
index 5d44437ca0..e4e159003f 100644
--- a/src/min_sd.cpp
+++ b/src/min_sd.cpp
@@ -11,10 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <mpi.h>
 #include "min_sd.h"
-#include "atom.h"
+#include <cmath>
 #include "update.h"
 #include "output.h"
 #include "timer.h"
diff --git a/src/minimize.cpp b/src/minimize.cpp
index e27fffd74b..94fdcd8681 100644
--- a/src/minimize.cpp
+++ b/src/minimize.cpp
@@ -11,7 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
 #include "minimize.h"
 #include "domain.h"
 #include "update.h"
@@ -53,9 +52,6 @@ void Minimize::command(int narg, char **arg)
   if (update->laststep < 0)
     error->all(FLERR,"Too many iterations");
 
-  if (lmp->kokkos)
-    error->all(FLERR,"Cannot yet use minimize with Kokkos");
-
   lmp->init();
   timer->init_timeout();
   update->minimize->setup();
diff --git a/src/modify.cpp b/src/modify.cpp
index 3f034bf034..109571d531 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
 #include "modify.h"
+#include <cstring>
 #include "style_compute.h"
 #include "style_fix.h"
 #include "atom.h"
@@ -798,7 +797,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
 
   const char *exceptions[] =
     {"GPU", "OMP", "INTEL", "property/atom", "cmap", "cmap3", "rx",
-     "deprecated", NULL};
+     "deprecated", "STORE/KIM", NULL};
 
   if (domain->box_exist == 0) {
     int m;
diff --git a/src/modify.h b/src/modify.h
index 5ff81855fe..b736485196 100644
--- a/src/modify.h
+++ b/src/modify.h
@@ -14,7 +14,6 @@
 #ifndef LMP_MODIFY_H
 #define LMP_MODIFY_H
 
-#include <cstdio>
 #include "pointers.h"
 #include <map>
 #include <string>
diff --git a/src/molecule.cpp b/src/molecule.cpp
index 454459084a..38887ebb0c 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -11,9 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "molecule.h"
+#include <mpi.h>
+#include <cctype>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
 #include "atom_vec_body.h"
@@ -21,12 +23,10 @@
 #include "comm.h"
 #include "domain.h"
 #include "math_extra.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 #define MAXLINE 256
 #define EPSILON 1.0e-7
diff --git a/src/mpiio.h b/src/mpiio.h
index 4953ade185..0098fca0e1 100644
--- a/src/mpiio.h
+++ b/src/mpiio.h
@@ -23,7 +23,7 @@
 #error "The MPIIO package cannot be compiled in serial with MPI STUBS"
 #endif
 
-#include "restart_mpiio.h"
+#include "restart_mpiio.h"  // IWYU pragma: export
 
 #else
 
diff --git a/src/my_pool_chunk.h b/src/my_pool_chunk.h
index 8bf88d35bb..a313e45f05 100644
--- a/src/my_pool_chunk.h
+++ b/src/my_pool_chunk.h
@@ -43,6 +43,10 @@ public variables:
 #ifndef LAMMPS_MY_POOL_CHUNK_H
 #define LAMMPS_MY_POOL_CHUNK_H
 
+#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32)
+#define LAMMPS_MEMALIGN 64
+#endif
+
 #include <cstdlib>
 
 namespace LAMMPS_NS {
@@ -190,9 +194,17 @@ class MyPoolChunk {
 
     for (int i = oldpage; i < npage; i++) {
       whichbin[i] = ibin;
+#if defined(LAMMPS_MEMALIGN)
+      void *ptr;
+      if (posix_memalign(&ptr, LAMMPS_MEMALIGN,
+                         chunkperpage*chunksize[ibin]*sizeof(T)))
+        errorflag = 2;
+      pages[i] = (T *) ptr;
+#else
       pages[i] = (T *) malloc(chunkperpage*chunksize[ibin]*sizeof(T));
       size += chunkperpage*chunksize[ibin];
       if (!pages[i]) errorflag = 2;
+#endif
     }
 
     // reset free list for unused chunks on new pages
diff --git a/src/nbin.cpp b/src/nbin.cpp
index 3e50148a04..4838d1d63d 100644
--- a/src/nbin.cpp
+++ b/src/nbin.cpp
@@ -12,10 +12,10 @@
 ------------------------------------------------------------------------- */
 
 #include "nbin.h"
+#include <cmath>
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "domain.h"
-#include "update.h"
 #include "memory.h"
 #include "error.h"
 
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index 6bdb9beae6..31720cc78c 100644
--- a/src/neigh_list.cpp
+++ b/src/neigh_list.cpp
@@ -12,15 +12,13 @@
 ------------------------------------------------------------------------- */
 
 #include "neigh_list.h"
+#include "my_page.h"    // IWYU pragma: keep
 #include "atom.h"
 #include "comm.h"
-#include "update.h"
-#include "pair.h"
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "my_page.h"
 #include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/neigh_list.h b/src/neigh_list.h
index 755a1bf134..aca11cd921 100644
--- a/src/neigh_list.h
+++ b/src/neigh_list.h
@@ -15,7 +15,6 @@
 #define LMP_NEIGH_LIST_H
 
 #include "pointers.h"
-#include "my_page.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 0382624198..d38aed08c0 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -15,11 +15,10 @@
    Contributing author (triclinic and multi-neigh) : Pieter in 't Veld (SNL)
 ------------------------------------------------------------------------- */
 
+#include "neighbor.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "nbin.h"
@@ -48,8 +47,6 @@
 #include "error.h"
 #include "utils.h"
 
-#include <map>
-
 using namespace LAMMPS_NS;
 using namespace NeighConst;
 
diff --git a/src/neighbor.h b/src/neighbor.h
index 3466dd426a..50de4b4c98 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -15,7 +15,6 @@
 #define LMP_NEIGHBOR_H
 
 #include "pointers.h"
-#include <map>
 
 namespace LAMMPS_NS {
 
diff --git a/src/npair.cpp b/src/npair.cpp
index 24cdc7750a..b63135fad6 100644
--- a/src/npair.cpp
+++ b/src/npair.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "npair.h"
+#include <cmath>
 #include "neighbor.h"
 #include "neigh_request.h"
 #include "nbin.h"
diff --git a/src/npair_copy.cpp b/src/npair_copy.cpp
index 9426d22ed3..0a522c628d 100644
--- a/src/npair_copy.cpp
+++ b/src/npair_copy.cpp
@@ -12,14 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_copy.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
-#include "my_page.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/npair_full_bin.cpp b/src/npair_full_bin.cpp
index 94a6af129c..464dca9251 100644
--- a/src/npair_full_bin.cpp
+++ b/src/npair_full_bin.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_full_bin.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_full_bin_atomonly.cpp b/src/npair_full_bin_atomonly.cpp
index db84733f1c..758fc7e42b 100644
--- a/src/npair_full_bin_atomonly.cpp
+++ b/src/npair_full_bin_atomonly.cpp
@@ -12,11 +12,9 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_full_bin_atomonly.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "domain.h"
 #include "my_page.h"
 #include "error.h"
 
diff --git a/src/npair_full_bin_ghost.cpp b/src/npair_full_bin_ghost.cpp
index 2edd03cc9e..61b27dd99d 100644
--- a/src/npair_full_bin_ghost.cpp
+++ b/src/npair_full_bin_ghost.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_full_bin_ghost.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp
index 9a2490ac5d..40ed2275be 100644
--- a/src/npair_full_multi.cpp
+++ b/src/npair_full_multi.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_full_multi.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_full_nsq.cpp b/src/npair_full_nsq.cpp
index 1b404ffc94..76b66fd004 100644
--- a/src/npair_full_nsq.cpp
+++ b/src/npair_full_nsq.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_full_nsq.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_full_nsq_ghost.cpp b/src/npair_full_nsq_ghost.cpp
index 1727b2905e..b20fa9b8ce 100644
--- a/src/npair_full_nsq_ghost.cpp
+++ b/src/npair_full_nsq_ghost.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_full_nsq_ghost.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_bin_atomonly_newton.cpp b/src/npair_half_bin_atomonly_newton.cpp
index 6da44b4a5c..a7fa3985ef 100644
--- a/src/npair_half_bin_atomonly_newton.cpp
+++ b/src/npair_half_bin_atomonly_newton.cpp
@@ -12,12 +12,9 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_bin_atomonly_newton.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
 #include "my_page.h"
 #include "error.h"
 
diff --git a/src/npair_half_bin_newtoff.cpp b/src/npair_half_bin_newtoff.cpp
index 4c44741ffe..65768918c9 100644
--- a/src/npair_half_bin_newtoff.cpp
+++ b/src/npair_half_bin_newtoff.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_bin_newtoff.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_bin_newtoff_ghost.cpp b/src/npair_half_bin_newtoff_ghost.cpp
index 72ec15e66a..91fbf049cb 100644
--- a/src/npair_half_bin_newtoff_ghost.cpp
+++ b/src/npair_half_bin_newtoff_ghost.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_bin_newtoff_ghost.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_bin_newton.cpp b/src/npair_half_bin_newton.cpp
index 3a387870e3..fe388e1144 100644
--- a/src/npair_half_bin_newton.cpp
+++ b/src/npair_half_bin_newton.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_bin_newton.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_bin_newton_tri.cpp b/src/npair_half_bin_newton_tri.cpp
index 169e710e0e..1f0e3c1187 100644
--- a/src/npair_half_bin_newton_tri.cpp
+++ b/src/npair_half_bin_newton_tri.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_bin_newton_tri.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp
index 07b5c87a6c..57dcf29cc7 100644
--- a/src/npair_half_multi_newtoff.cpp
+++ b/src/npair_half_multi_newtoff.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_multi_newtoff.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp
index 3d90979329..a9293d3d64 100644
--- a/src/npair_half_multi_newton.cpp
+++ b/src/npair_half_multi_newton.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_multi_newton.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp
index 909c69246b..c1d845cb38 100644
--- a/src/npair_half_multi_newton_tri.cpp
+++ b/src/npair_half_multi_newton_tri.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_multi_newton_tri.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_nsq_newtoff.cpp b/src/npair_half_nsq_newtoff.cpp
index 06e8344332..db369687d0 100644
--- a/src/npair_half_nsq_newtoff.cpp
+++ b/src/npair_half_nsq_newtoff.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_nsq_newtoff.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_nsq_newtoff_ghost.cpp b/src/npair_half_nsq_newtoff_ghost.cpp
index 1865061a8b..0a9b6d0f45 100644
--- a/src/npair_half_nsq_newtoff_ghost.cpp
+++ b/src/npair_half_nsq_newtoff_ghost.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_nsq_newtoff_ghost.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_nsq_newton.cpp b/src/npair_half_nsq_newton.cpp
index 11c71d5609..69489915b2 100644
--- a/src/npair_half_nsq_newton.cpp
+++ b/src/npair_half_nsq_newton.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_nsq_newton.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_respa_bin_newtoff.cpp b/src/npair_half_respa_bin_newtoff.cpp
index 0145771f4a..8c1d8d684f 100644
--- a/src/npair_half_respa_bin_newtoff.cpp
+++ b/src/npair_half_respa_bin_newtoff.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_respa_bin_newtoff.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_respa_bin_newton.cpp b/src/npair_half_respa_bin_newton.cpp
index 72a613204d..d2598fa1a4 100644
--- a/src/npair_half_respa_bin_newton.cpp
+++ b/src/npair_half_respa_bin_newton.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_respa_bin_newton.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_respa_bin_newton_tri.cpp b/src/npair_half_respa_bin_newton_tri.cpp
index add1cf6e5c..efe48d48e1 100644
--- a/src/npair_half_respa_bin_newton_tri.cpp
+++ b/src/npair_half_respa_bin_newton_tri.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_respa_bin_newton_tri.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_respa_nsq_newtoff.cpp b/src/npair_half_respa_nsq_newtoff.cpp
index c0e932f0ae..334ebb5ca8 100644
--- a/src/npair_half_respa_nsq_newtoff.cpp
+++ b/src/npair_half_respa_nsq_newtoff.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_respa_nsq_newtoff.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_respa_nsq_newton.cpp b/src/npair_half_respa_nsq_newton.cpp
index f7d161896d..7ecd02b0c5 100644
--- a/src/npair_half_respa_nsq_newton.cpp
+++ b/src/npair_half_respa_nsq_newton.cpp
@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_respa_nsq_newton.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp
index 021452028b..b9e44675ac 100644
--- a/src/npair_half_size_bin_newtoff.cpp
+++ b/src/npair_half_size_bin_newtoff.cpp
@@ -11,9 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "npair_half_size_bin_newtoff.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp
index 760c09570a..93bcc25373 100644
--- a/src/npair_half_size_bin_newton.cpp
+++ b/src/npair_half_size_bin_newton.cpp
@@ -11,9 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "npair_half_size_bin_newton.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_size_bin_newton_tri.cpp b/src/npair_half_size_bin_newton_tri.cpp
index d831982ed6..39068c02bc 100644
--- a/src/npair_half_size_bin_newton_tri.cpp
+++ b/src/npair_half_size_bin_newton_tri.cpp
@@ -11,9 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "npair_half_size_bin_newton_tri.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_size_nsq_newtoff.cpp b/src/npair_half_size_nsq_newtoff.cpp
index 1c2fe5f3d5..6f169d0b6c 100644
--- a/src/npair_half_size_nsq_newtoff.cpp
+++ b/src/npair_half_size_nsq_newtoff.cpp
@@ -11,9 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "npair_half_size_nsq_newtoff.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_half_size_nsq_newton.cpp b/src/npair_half_size_nsq_newton.cpp
index ce9f8ec186..d427c14809 100644
--- a/src/npair_half_size_nsq_newton.cpp
+++ b/src/npair_half_size_nsq_newton.cpp
@@ -11,9 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "npair_half_size_nsq_newton.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_halffull_newtoff.cpp b/src/npair_halffull_newtoff.cpp
index 84816f07b2..6ff5433e88 100644
--- a/src/npair_halffull_newtoff.cpp
+++ b/src/npair_halffull_newtoff.cpp
@@ -12,12 +12,8 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_halffull_newtoff.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "atom.h"
 #include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
 #include "my_page.h"
 #include "error.h"
 
diff --git a/src/npair_halffull_newton.cpp b/src/npair_halffull_newton.cpp
index 371bbd33a8..0912cfe12f 100644
--- a/src/npair_halffull_newton.cpp
+++ b/src/npair_halffull_newton.cpp
@@ -12,12 +12,9 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_halffull_newton.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
 #include "my_page.h"
 #include "error.h"
 
diff --git a/src/npair_skip.cpp b/src/npair_skip.cpp
index 1fe202537a..028041a947 100644
--- a/src/npair_skip.cpp
+++ b/src/npair_skip.cpp
@@ -12,12 +12,9 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_skip.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
 #include "my_page.h"
 #include "error.h"
 
diff --git a/src/npair_skip_respa.cpp b/src/npair_skip_respa.cpp
index 1d4eda5354..68436654b2 100644
--- a/src/npair_skip_respa.cpp
+++ b/src/npair_skip_respa.cpp
@@ -12,12 +12,9 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_skip_respa.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "molecule.h"
-#include "domain.h"
 #include "my_page.h"
 #include "error.h"
 
diff --git a/src/npair_skip_size.cpp b/src/npair_skip_size.cpp
index 67717ae576..436d21f76f 100644
--- a/src/npair_skip_size.cpp
+++ b/src/npair_skip_size.cpp
@@ -11,9 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "npair_skip_size.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_skip_size_off2on.cpp b/src/npair_skip_size_off2on.cpp
index 74a80e6d3d..cd674ff777 100644
--- a/src/npair_skip_size_off2on.cpp
+++ b/src/npair_skip_size_off2on.cpp
@@ -11,9 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "npair_skip_size_off2on.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp
index a042acd1c6..0540592cba 100644
--- a/src/npair_skip_size_off2on_oneside.cpp
+++ b/src/npair_skip_size_off2on_oneside.cpp
@@ -11,9 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "npair_skip_size_off2on_oneside.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "atom.h"
 #include "atom_vec.h"
diff --git a/src/nstencil_full_bin_2d.cpp b/src/nstencil_full_bin_2d.cpp
index 0986c40dd4..b18d990bba 100644
--- a/src/nstencil_full_bin_2d.cpp
+++ b/src/nstencil_full_bin_2d.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_full_bin_2d.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/nstencil_full_bin_3d.cpp b/src/nstencil_full_bin_3d.cpp
index b6a2198132..46ec073ddd 100644
--- a/src/nstencil_full_bin_3d.cpp
+++ b/src/nstencil_full_bin_3d.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_full_bin_3d.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/nstencil_full_ghost_bin_2d.cpp b/src/nstencil_full_ghost_bin_2d.cpp
index bbbf1a4466..5ac19569c5 100644
--- a/src/nstencil_full_ghost_bin_2d.cpp
+++ b/src/nstencil_full_ghost_bin_2d.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_full_ghost_bin_2d.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/nstencil_full_ghost_bin_3d.cpp b/src/nstencil_full_ghost_bin_3d.cpp
index e9abca2174..6ee56516dc 100644
--- a/src/nstencil_full_ghost_bin_3d.cpp
+++ b/src/nstencil_full_ghost_bin_3d.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_full_ghost_bin_3d.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp
index ed2ffe11dc..c69c53a761 100644
--- a/src/nstencil_full_multi_2d.cpp
+++ b/src/nstencil_full_multi_2d.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_full_multi_2d.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 #include "atom.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp
index c171bfadc5..df47c1e7e9 100644
--- a/src/nstencil_full_multi_3d.cpp
+++ b/src/nstencil_full_multi_3d.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_full_multi_3d.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 #include "atom.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/nstencil_half_bin_2d_newtoff.cpp b/src/nstencil_half_bin_2d_newtoff.cpp
index e51db6fe7a..f3a6c5d08b 100644
--- a/src/nstencil_half_bin_2d_newtoff.cpp
+++ b/src/nstencil_half_bin_2d_newtoff.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_bin_2d_newtoff.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/nstencil_half_bin_2d_newton.cpp b/src/nstencil_half_bin_2d_newton.cpp
index 9479bbf0c8..8fdc8f1aa9 100644
--- a/src/nstencil_half_bin_2d_newton.cpp
+++ b/src/nstencil_half_bin_2d_newton.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_bin_2d_newton.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/nstencil_half_bin_2d_newton_tri.cpp b/src/nstencil_half_bin_2d_newton_tri.cpp
index 4f89b1c326..30d064fb29 100644
--- a/src/nstencil_half_bin_2d_newton_tri.cpp
+++ b/src/nstencil_half_bin_2d_newton_tri.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_bin_2d_newton_tri.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/nstencil_half_bin_3d_newtoff.cpp b/src/nstencil_half_bin_3d_newtoff.cpp
index 433de400c2..e44a93d47d 100644
--- a/src/nstencil_half_bin_3d_newtoff.cpp
+++ b/src/nstencil_half_bin_3d_newtoff.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_bin_3d_newtoff.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/nstencil_half_bin_3d_newton.cpp b/src/nstencil_half_bin_3d_newton.cpp
index 24c234c004..998ed28afe 100644
--- a/src/nstencil_half_bin_3d_newton.cpp
+++ b/src/nstencil_half_bin_3d_newton.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_bin_3d_newton.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/nstencil_half_bin_3d_newton_tri.cpp b/src/nstencil_half_bin_3d_newton_tri.cpp
index 691ce0bb80..2aae44ceaf 100644
--- a/src/nstencil_half_bin_3d_newton_tri.cpp
+++ b/src/nstencil_half_bin_3d_newton_tri.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_bin_3d_newton_tri.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/nstencil_half_ghost_bin_2d_newtoff.cpp b/src/nstencil_half_ghost_bin_2d_newtoff.cpp
index 4bb0ecafe2..6f9a7585fe 100644
--- a/src/nstencil_half_ghost_bin_2d_newtoff.cpp
+++ b/src/nstencil_half_ghost_bin_2d_newtoff.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_ghost_bin_2d_newtoff.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/nstencil_half_ghost_bin_3d_newtoff.cpp b/src/nstencil_half_ghost_bin_3d_newtoff.cpp
index 1026b11542..6492fe4a4e 100644
--- a/src/nstencil_half_ghost_bin_3d_newtoff.cpp
+++ b/src/nstencil_half_ghost_bin_3d_newtoff.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_ghost_bin_3d_newtoff.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/nstencil_half_multi_2d_newtoff.cpp b/src/nstencil_half_multi_2d_newtoff.cpp
index 567abe2878..63cd3fd524 100644
--- a/src/nstencil_half_multi_2d_newtoff.cpp
+++ b/src/nstencil_half_multi_2d_newtoff.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_multi_2d_newtoff.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 #include "atom.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/nstencil_half_multi_2d_newton.cpp b/src/nstencil_half_multi_2d_newton.cpp
index 5dc2c37148..f6f6c488a5 100644
--- a/src/nstencil_half_multi_2d_newton.cpp
+++ b/src/nstencil_half_multi_2d_newton.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_multi_2d_newton.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 #include "atom.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/nstencil_half_multi_2d_newton_tri.cpp b/src/nstencil_half_multi_2d_newton_tri.cpp
index 59a5a1d19e..b44ab36ea0 100644
--- a/src/nstencil_half_multi_2d_newton_tri.cpp
+++ b/src/nstencil_half_multi_2d_newton_tri.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_multi_2d_newton_tri.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 #include "atom.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/nstencil_half_multi_3d_newtoff.cpp b/src/nstencil_half_multi_3d_newtoff.cpp
index 72b882dddc..5a83c4e002 100644
--- a/src/nstencil_half_multi_3d_newtoff.cpp
+++ b/src/nstencil_half_multi_3d_newtoff.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_multi_3d_newtoff.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 #include "atom.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/nstencil_half_multi_3d_newton.cpp b/src/nstencil_half_multi_3d_newton.cpp
index 9a5d5cab65..5b0c7f9f63 100644
--- a/src/nstencil_half_multi_3d_newton.cpp
+++ b/src/nstencil_half_multi_3d_newton.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_multi_3d_newton.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 #include "atom.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/nstencil_half_multi_3d_newton_tri.cpp b/src/nstencil_half_multi_3d_newton_tri.cpp
index 953beb3211..b25a0d0bdb 100644
--- a/src/nstencil_half_multi_3d_newton_tri.cpp
+++ b/src/nstencil_half_multi_3d_newton_tri.cpp
@@ -12,8 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "nstencil_half_multi_3d_newton_tri.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 #include "atom.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/ntopo.cpp b/src/ntopo.cpp
index 8a87a5d6e5..ca63b85328 100644
--- a/src/ntopo.cpp
+++ b/src/ntopo.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "ntopo.h"
+#include <mpi.h>
 #include "atom.h"
 #include "neighbor.h"
 #include "comm.h"
diff --git a/src/ntopo_angle_all.cpp b/src/ntopo_angle_all.cpp
index 2a358c8ce5..e0c20609a1 100644
--- a/src/ntopo_angle_all.cpp
+++ b/src/ntopo_angle_all.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "ntopo_angle_all.h"
+#include <mpi.h>
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
diff --git a/src/ntopo_angle_partial.cpp b/src/ntopo_angle_partial.cpp
index c82110cda5..a6fd900825 100644
--- a/src/ntopo_angle_partial.cpp
+++ b/src/ntopo_angle_partial.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "ntopo_angle_partial.h"
+#include <mpi.h>
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
diff --git a/src/ntopo_angle_template.cpp b/src/ntopo_angle_template.cpp
index 15a8b658f3..8cbcf8bcbd 100644
--- a/src/ntopo_angle_template.cpp
+++ b/src/ntopo_angle_template.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "ntopo_angle_template.h"
+#include <mpi.h>
 #include "atom.h"
 #include "atom_vec.h"
 #include "force.h"
diff --git a/src/ntopo_bond_all.cpp b/src/ntopo_bond_all.cpp
index 42e9e2303d..5309754554 100644
--- a/src/ntopo_bond_all.cpp
+++ b/src/ntopo_bond_all.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "ntopo_bond_all.h"
+#include <mpi.h>
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
diff --git a/src/ntopo_bond_partial.cpp b/src/ntopo_bond_partial.cpp
index 5a1acd9191..1cbf5eed11 100644
--- a/src/ntopo_bond_partial.cpp
+++ b/src/ntopo_bond_partial.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "ntopo_bond_partial.h"
+#include <mpi.h>
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
diff --git a/src/ntopo_bond_template.cpp b/src/ntopo_bond_template.cpp
index fa98658ad0..cd7b85aa19 100644
--- a/src/ntopo_bond_template.cpp
+++ b/src/ntopo_bond_template.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "ntopo_bond_template.h"
+#include <mpi.h>
 #include "atom.h"
 #include "atom_vec.h"
 #include "force.h"
diff --git a/src/ntopo_dihedral_all.cpp b/src/ntopo_dihedral_all.cpp
index 9c94fb10f9..5af2d526e0 100644
--- a/src/ntopo_dihedral_all.cpp
+++ b/src/ntopo_dihedral_all.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "ntopo_dihedral_all.h"
+#include <mpi.h>
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp
index 14749e6511..faac57aa51 100644
--- a/src/ntopo_dihedral_partial.cpp
+++ b/src/ntopo_dihedral_partial.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "ntopo_dihedral_partial.h"
+#include <mpi.h>
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp
index 8ea860c2e2..bce8ecf4bc 100644
--- a/src/ntopo_dihedral_template.cpp
+++ b/src/ntopo_dihedral_template.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "ntopo_dihedral_template.h"
+#include <mpi.h>
 #include "atom.h"
 #include "atom_vec.h"
 #include "force.h"
diff --git a/src/ntopo_improper_all.cpp b/src/ntopo_improper_all.cpp
index 6c478dec52..0cbecbf962 100644
--- a/src/ntopo_improper_all.cpp
+++ b/src/ntopo_improper_all.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "ntopo_improper_all.h"
+#include <mpi.h>
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp
index 2c37668ca8..17e5d4cf62 100644
--- a/src/ntopo_improper_partial.cpp
+++ b/src/ntopo_improper_partial.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "ntopo_improper_partial.h"
+#include <mpi.h>
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp
index 953e010d89..a80fe60e1d 100644
--- a/src/ntopo_improper_template.cpp
+++ b/src/ntopo_improper_template.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
 #include "ntopo_improper_template.h"
+#include <mpi.h>
 #include "atom.h"
 #include "atom_vec.h"
 #include "force.h"
diff --git a/src/output.cpp b/src/output.cpp
index 6253d7de37..193db9ae2a 100644
--- a/src/output.cpp
+++ b/src/output.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "output.h"
+#include <mpi.h>
+#include <cstring>
 #include "style_dump.h"
 #include "atom.h"
 #include "neighbor.h"
@@ -26,7 +25,6 @@
 #include "domain.h"
 #include "thermo.h"
 #include "modify.h"
-#include "compute.h"
 #include "force.h"
 #include "dump.h"
 #include "write_restart.h"
diff --git a/src/pair.cpp b/src/pair.cpp
index 2b4863a54c..7c8424ce18 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -15,24 +15,18 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cctype>
-#include <cfloat>
-#include <climits>
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair.h"
+#include <mpi.h>
+#include <cfloat>    // IWYU pragma: keep
+#include <climits>   // IWYU pragma: keep
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "neighbor.h"
-#include "neigh_list.h"
 #include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "kspace.h"
-#include "update.h"
-#include "modify.h"
 #include "compute.h"
 #include "suffix.h"
 #include "atom_masks.h"
@@ -60,6 +54,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
   comm_forward = comm_reverse = comm_reverse_off = 0;
 
   single_enable = 1;
+  single_hessian_enable = 0;
   restartinfo = 1;
   respa_enable = 0;
   one_coeff = 0;
@@ -1749,6 +1744,18 @@ void Pair::init_bitmap(double inner, double outer, int ntablebits,
 
 /* ---------------------------------------------------------------------- */
 
+void Pair::hessian_twobody(double fforce, double dfac, double delr[3], double phiTensor[6]) {
+  int m = 0;
+  for (int k=0; k<3; k++) {
+    phiTensor[m] = fforce;
+    for (int l=k; l<3; l++) {
+      if (l>k) phiTensor[m] = 0;
+      phiTensor[m++] += delr[k]*delr[l] * dfac;
+    }
+  }
+}
+/* ---------------------------------------------------------------------- */
+
 double Pair::memory_usage()
 {
   double bytes = comm->nthreads*maxeatom * sizeof(double);
diff --git a/src/pair.h b/src/pair.h
index bad2b83c74..a0269bd5b2 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -14,7 +14,7 @@
 #ifndef LMP_PAIR_H
 #define LMP_PAIR_H
 
-#include "pointers.h"
+#include "pointers.h"  // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
@@ -46,6 +46,7 @@ class Pair : protected Pointers {
   int comm_reverse_off;          // size of reverse comm even if newton off
 
   int single_enable;             // 1 if single() routine exists
+  int single_hessian_enable;     // 1 if single_hessian() routine exists
   int restartinfo;               // 1 if pair style writes restart info
   int respa_enable;              // 1 if inner/middle/outer rRESPA routines
   int one_coeff;                 // 1 if allows only one coeff * * call
@@ -148,6 +149,16 @@ class Pair : protected Pointers {
     return 0.0;
   }
 
+  void hessian_twobody(double fforce, double dfac, double delr[3], double phiTensor[6]);
+
+  virtual double single_hessian(int, int, int, int,
+                        double, double[3], double, double,
+                        double& fforce, double d2u[6]) {
+    fforce = 0.0;
+    for (int i=0; i<6; i++) d2u[i] = 0;
+    return 0.0;
+  }
+
   virtual void settings(int, char **) = 0;
   virtual void coeff(int, char **) = 0;
 
diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp
index 17731ebf0b..b94436b696 100644
--- a/src/pair_beck.cpp
+++ b/src/pair_beck.cpp
@@ -15,10 +15,9 @@
    Contributing author: Jonathan Zimmerman (Sandia)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include "pair_beck.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_born.cpp b/src/pair_born.cpp
index 78434c91f8..bd993acb56 100644
--- a/src/pair_born.cpp
+++ b/src/pair_born.cpp
@@ -15,11 +15,10 @@
    Contributing Author: Sai Jayaraman (Sandia)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_born.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp
index 2e565897b5..f7e139c750 100644
--- a/src/pair_born_coul_dsf.cpp
+++ b/src/pair_born_coul_dsf.cpp
@@ -16,11 +16,9 @@
    References: Fennell and Gezelter, JCP 124, 234104 (2006)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_born_coul_dsf.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp
index 3bb0e39e57..f4d533bdb0 100644
--- a/src/pair_born_coul_wolf.cpp
+++ b/src/pair_born_coul_wolf.cpp
@@ -15,11 +15,9 @@
    Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_born_coul_wolf.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp
index a3cf1a38d6..a94ce87891 100644
--- a/src/pair_buck.cpp
+++ b/src/pair_buck.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_buck.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp
index 094797694c..d05c139f71 100644
--- a/src/pair_buck_coul_cut.cpp
+++ b/src/pair_buck_coul_cut.cpp
@@ -15,10 +15,9 @@
    Contributing author: Eduardo Bringa (LLNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include "pair_buck_coul_cut.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp
index 196e064219..9e6f238eba 100644
--- a/src/pair_coul_cut.cpp
+++ b/src/pair_coul_cut.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_cut.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp
index c8afdabb93..1b87a93701 100644
--- a/src/pair_coul_debye.cpp
+++ b/src/pair_coul_debye.cpp
@@ -11,17 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_debye.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp
index e487ff171c..22230182b0 100644
--- a/src/pair_coul_dsf.cpp
+++ b/src/pair_coul_dsf.cpp
@@ -16,11 +16,10 @@
    References: Fennell and Gezelter, JCP 124, 234104 (2006)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_dsf.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp
index 282c855249..628f6a6b36 100644
--- a/src/pair_coul_streitz.cpp
+++ b/src/pair_coul_streitz.cpp
@@ -15,11 +15,11 @@
    Contributing author: Ray Shan (Sandia)
 ------------------------------------------------------------------------- */
 
+#include "pair_coul_streitz.h"
+#include <mpi.h>
 #include <cmath>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "pair_coul_streitz.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -27,8 +27,6 @@
 #include "neighbor.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "group.h"
-#include "update.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp
index dbf21b8bee..15c7839fc6 100644
--- a/src/pair_coul_wolf.cpp
+++ b/src/pair_coul_wolf.cpp
@@ -15,11 +15,9 @@
    Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_coul_wolf.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp
index 0b1342fb2d..058809eb80 100644
--- a/src/pair_deprecated.cpp
+++ b/src/pair_deprecated.cpp
@@ -15,8 +15,8 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "pair_deprecated.h"
+#include <cstring>
 #include "pair_hybrid.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp
index 914b4aee17..ec65eaafd6 100644
--- a/src/pair_dpd.cpp
+++ b/src/pair_dpd.cpp
@@ -15,12 +15,10 @@
    Contributing author: Kurt Smith (U Pittsburgh)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include "pair_dpd.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
-#include "atom_vec.h"
 #include "comm.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp
index 1207c954eb..15d7c90b27 100644
--- a/src/pair_dpd_tstat.cpp
+++ b/src/pair_dpd_tstat.cpp
@@ -11,8 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
 #include "pair_dpd_tstat.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp
index 2d157d6cac..7fd3233f4c 100644
--- a/src/pair_gauss.cpp
+++ b/src/pair_gauss.cpp
@@ -15,15 +15,13 @@
    Contributing author: Sai Jayaraman (Sandia)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_gauss.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp
index 9aff8a387a..762b9fe8fc 100644
--- a/src/pair_hybrid.cpp
+++ b/src/pair_hybrid.cpp
@@ -12,11 +12,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
+#include "pair_hybrid.h"
+#include <mpi.h>
 #include <cstring>
 #include <cctype>
-#include "pair_hybrid.h"
 #include "atom.h"
 #include "force.h"
 #include "pair.h"
diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h
index e313e16f18..074517a859 100644
--- a/src/pair_hybrid.h
+++ b/src/pair_hybrid.h
@@ -20,7 +20,6 @@ PairStyle(hybrid,PairHybrid)
 #ifndef LMP_PAIR_HYBRID_H
 #define LMP_PAIR_HYBRID_H
 
-#include <cstdio>
 #include "pair.h"
 
 namespace LAMMPS_NS {
diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp
index 717c0de1d1..e67cb677af 100644
--- a/src/pair_hybrid_overlay.cpp
+++ b/src/pair_hybrid_overlay.cpp
@@ -11,14 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
+#include "pair_hybrid_overlay.h"
 #include <cstring>
 #include <cctype>
-#include "pair_hybrid_overlay.h"
 #include "atom.h"
 #include "force.h"
-#include "neighbor.h"
-#include "neigh_request.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp
index cefe9b87e0..c27038900d 100644
--- a/src/pair_lj96_cut.cpp
+++ b/src/pair_lj96_cut.cpp
@@ -15,11 +15,10 @@
    Contributing author: Chuanfu Luo (luochuanfu@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj96_cut.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -27,7 +26,6 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "math_const.h"
 #include "memory.h"
diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp
index fdbfca608f..7990952494 100644
--- a/src/pair_lj_cubic.cpp
+++ b/src/pair_lj_cubic.cpp
@@ -16,15 +16,12 @@
    Contributing author: Aidan Thompson (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cubic.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp
index 2a0fcde3a5..0302858adb 100644
--- a/src/pair_lj_cut.cpp
+++ b/src/pair_lj_cut.cpp
@@ -15,11 +15,10 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -27,7 +26,6 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "math_const.h"
 #include "memory.h"
diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp
index 38a6e2c431..d4640bee3a 100644
--- a/src/pair_lj_cut_coul_cut.cpp
+++ b/src/pair_lj_cut_coul_cut.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_coul_cut.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp
index cc6e92b2e3..4ef533a743 100644
--- a/src/pair_lj_cut_coul_debye.cpp
+++ b/src/pair_lj_cut_coul_debye.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_lj_cut_coul_debye.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "neigh_list.h"
 #include "force.h"
diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp
index f114a5851f..778f9f2fb4 100644
--- a/src/pair_lj_cut_coul_dsf.cpp
+++ b/src/pair_lj_cut_coul_dsf.cpp
@@ -16,11 +16,10 @@
    References: Fennell and Gezelter, JCP 124, 234104 (2006)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_coul_dsf.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp
index 55aff0d7c5..00a5832529 100644
--- a/src/pair_lj_cut_coul_wolf.cpp
+++ b/src/pair_lj_cut_coul_wolf.cpp
@@ -15,19 +15,14 @@
    Contributing author: Vishal Boddu (FAU)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_cut_coul_wolf.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp
index d5c0a40f2d..a5184bc2f5 100644
--- a/src/pair_lj_expand.cpp
+++ b/src/pair_lj_expand.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_expand.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp
index 1fdaefebe9..baef482ef9 100644
--- a/src/pair_lj_gromacs.cpp
+++ b/src/pair_lj_gromacs.cpp
@@ -15,15 +15,12 @@
    Contributing author: Mark Stevens (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_gromacs.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp
index 28dc8ec79b..c62944b6a1 100644
--- a/src/pair_lj_gromacs_coul_gromacs.cpp
+++ b/src/pair_lj_gromacs_coul_gromacs.cpp
@@ -15,11 +15,9 @@
    Contributing author: Mark Stevens (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_gromacs_coul_gromacs.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp
index ecacadbffa..7c7eb51b53 100644
--- a/src/pair_lj_smooth.cpp
+++ b/src/pair_lj_smooth.cpp
@@ -15,10 +15,9 @@
    Contributing author: Craig Maloney (UCSB)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include "pair_lj_smooth.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp
index 265828c4cf..bc2904c262 100644
--- a/src/pair_lj_smooth_linear.cpp
+++ b/src/pair_lj_smooth_linear.cpp
@@ -15,10 +15,9 @@
    Contributing author: Jonathan Zimmerman (Sandia)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
 #include "pair_lj_smooth_linear.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -30,7 +29,9 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-PairLJSmoothLinear::PairLJSmoothLinear(LAMMPS *lmp) : Pair(lmp) {}
+PairLJSmoothLinear::PairLJSmoothLinear(LAMMPS *lmp) : Pair(lmp) {
+  single_hessian_enable = 1;
+}
 
 /* ---------------------------------------------------------------------- */
 
@@ -346,3 +347,26 @@ double PairLJSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype,
 
   return factor_lj*philj;
 }
+
+double PairLJSmoothLinear::single_hessian(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+                         double delr[3], double /*factor_coul*/, double factor_lj,
+                         double &fforce, double d2u[6])
+{
+  double r2inv,r6inv,forcelj,philj,r,rinv;
+
+  r2inv = 1.0/rsq;
+  r6inv = r2inv*r2inv*r2inv;
+  rinv  = sqrt(r2inv);
+  r     = sqrt(rsq);
+  forcelj = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
+  forcelj = rinv*forcelj - dljcut[itype][jtype];
+  fforce = factor_lj*forcelj*rinv;
+
+  philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
+  philj = philj - ljcut[itype][jtype]
+                + (r-cut[itype][jtype])*dljcut[itype][jtype];
+
+  double d2r = factor_lj * r6inv * (13.0*lj1[itype][jtype]*r6inv - 7.0*lj2[itype][jtype])/rsq;
+  hessian_twobody(fforce, -(fforce + d2r) / rsq, delr, d2u);
+  return factor_lj*philj;
+}
diff --git a/src/pair_lj_smooth_linear.h b/src/pair_lj_smooth_linear.h
index c18c442a18..7e26a7011e 100644
--- a/src/pair_lj_smooth_linear.h
+++ b/src/pair_lj_smooth_linear.h
@@ -38,6 +38,7 @@ class PairLJSmoothLinear : public Pair {
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
   double single(int, int, int, int, double, double, double, double &);
+  double single_hessian(int, int, int, int, double, double[3], double, double, double&, double[6]);
 
  protected:
   double cut_global;
diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp
index 231832dc48..46657687f6 100644
--- a/src/pair_mie_cut.cpp
+++ b/src/pair_mie_cut.cpp
@@ -15,11 +15,10 @@
    Contributing author: Cassiano Aimoli (aimoli@gmail.com)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_mie_cut.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -27,7 +26,6 @@
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "update.h"
-#include "integrate.h"
 #include "respa.h"
 #include "math_const.h"
 #include "memory.h"
diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp
index dca1834c14..d088f98bf4 100644
--- a/src/pair_morse.cpp
+++ b/src/pair_morse.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_morse.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp
index 7602f7b925..6f821e684b 100644
--- a/src/pair_soft.cpp
+++ b/src/pair_soft.cpp
@@ -11,15 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_soft.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "update.h"
 #include "neigh_list.h"
 #include "math_const.h"
 #include "memory.h"
diff --git a/src/pair_table.cpp b/src/pair_table.cpp
index b1b6f45eda..9fcbc3ee9f 100644
--- a/src/pair_table.cpp
+++ b/src/pair_table.cpp
@@ -15,11 +15,12 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
+#include "pair_table.h"
 #include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
-#include "pair_table.h"
+#include <string>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp
index 226fb6e7d9..8cc4d2796f 100644
--- a/src/pair_ufm.cpp
+++ b/src/pair_ufm.cpp
@@ -17,26 +17,18 @@
             Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
  ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_ufm.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp
index 913afbd5a1..e8775c9668 100644
--- a/src/pair_yukawa.cpp
+++ b/src/pair_yukawa.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
 #include "pair_yukawa.h"
+#include <mpi.h>
+#include <cmath>
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp
index 254a82ea64..199e4f0907 100644
--- a/src/pair_zbl.cpp
+++ b/src/pair_zbl.cpp
@@ -15,21 +15,12 @@
    Contributing authors: Stephen Foiles, Aidan Thompson (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_zbl.h"
+#include <cmath>
 #include "atom.h"
-#include "comm.h"
 #include "force.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "integrate.h"
-#include "respa.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
 
@@ -37,7 +28,6 @@
 // "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985.
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
 using namespace PairZBLConstants;
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp
index 143808f598..403bd73944 100644
--- a/src/pair_zero.cpp
+++ b/src/pair_zero.cpp
@@ -15,11 +15,9 @@
    Contributing author: Carsten Svaneborg (SDU)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_zero.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
diff --git a/src/pointers.h b/src/pointers.h
index 44967f5135..2d528db392 100644
--- a/src/pointers.h
+++ b/src/pointers.h
@@ -21,9 +21,11 @@
 #ifndef LMP_POINTERS_H
 #define LMP_POINTERS_H
 
-#include "lmptype.h"
-#include <mpi.h>
-#include "lammps.h"
+#include "lmptype.h"   // IWYU pragma: export
+#include <mpi.h>       // IWYU pragma: export
+#include <cstddef>     // IWYU pragme: export
+#include <cstdio>      // IWYU pragma: export
+#include "lammps.h"    // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
@@ -34,6 +36,15 @@ namespace LAMMPS_NS {
 #define MIN(A,B) ((A) < (B) ? (A) : (B))
 #define MAX(A,B) ((A) > (B) ? (A) : (B))
 
+// enum used for KOKKOS host/device flags
+
+enum ExecutionSpace{Host,Device};
+
+// global forward declarations
+
+template <class T> class MyPoolChunk;
+template <class T> class MyPage;
+
 class Pointers {
  public:
   Pointers(LAMMPS *ptr) :
diff --git a/src/procmap.cpp b/src/procmap.cpp
index 8207b61f4c..1741e351fe 100644
--- a/src/procmap.cpp
+++ b/src/procmap.cpp
@@ -16,6 +16,12 @@
 ------------------------------------------------------------------------- */
 
 #include "procmap.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <map>
+#include <string>
+#include <utility>
 #include "universe.h"
 #include "comm.h"
 #include "domain.h"
@@ -23,9 +29,6 @@
 #include "memory.h"
 #include "error.h"
 
-#include <map>
-#include <string>
-
 using namespace LAMMPS_NS;
 
 #define MAXLINE 128
diff --git a/src/random_mars.cpp b/src/random_mars.cpp
index 464e640eab..9de5290d29 100644
--- a/src/random_mars.cpp
+++ b/src/random_mars.cpp
@@ -14,8 +14,8 @@
 // Marsaglia random number generator
 // see RANMAR in F James, Comp Phys Comm, 60, 329 (1990)
 
-#include <cmath>
 #include "random_mars.h"
+#include <cmath>
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/random_park.cpp b/src/random_park.cpp
index fc00939bd4..e12e8a3a10 100644
--- a/src/random_park.cpp
+++ b/src/random_park.cpp
@@ -13,8 +13,8 @@
 
 // Park/Miller RNG
 
-#include <cmath>
 #include "random_park.h"
+#include <cmath>
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/rcb.cpp b/src/rcb.cpp
index 83cdccdf80..2cc70a2de9 100644
--- a/src/rcb.cpp
+++ b/src/rcb.cpp
@@ -11,12 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "rcb.h"
 #include <mpi.h>
 #include <cstring>
-#include "rcb.h"
 #include "irregular.h"
 #include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
@@ -473,6 +472,24 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
     valuehalf = valuehalf_select;
     if (ndot > 0) memcpy(dotmark,dotmark_select,ndot*sizeof(int));
 
+    // special case for zero box width
+    // can occur when all dots are on corner vertices of this sub-box
+    // split box on longest dimension
+    // reset dotmark for that cut
+
+    if (largest == 0.0) {
+      dim = 0;
+      if (hi[1]-lo[1] > hi[0]-lo[0]) dim = 1;
+      if (dimension == 3 && hi[2]-lo[2] > hi[dim]-lo[dim]) dim = 2;
+      valuehalf = 0.5* (lo[dim] + hi[dim]);
+
+      for (j = 0; j < nlist; j++) {
+        i = dotlist[j];
+        if (dots[i].x[dim] <= valuehalf) dotmark[i] = 0;
+        else dotmark[i] = 1;
+      }
+    }
+
     // found median
     // store cut info only if I am procmid
 
diff --git a/src/rcb.h b/src/rcb.h
index f65ee2388a..555c4142b5 100644
--- a/src/rcb.h
+++ b/src/rcb.h
@@ -14,7 +14,6 @@
 #ifndef LAMMPS_RCB_H
 #define LAMMPS_RCB_H
 
-#include <mpi.h>
 #include "pointers.h"
 
 namespace LAMMPS_NS {
diff --git a/src/read_data.cpp b/src/read_data.cpp
index 989f989269..1208ab4b43 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -15,19 +15,15 @@
 // due to OpenMPI bug which sets INT64_MAX via its mpi.h
 //   before lmptype.h can set flags to insure it is done correctly
 
-#include "lmptype.h"
-#include <mpi.h>
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
-#include <cctype>
 #include "read_data.h"
+#include <mpi.h>
+#include <cstring>
+#include <cctype>
 #include "atom.h"
 #include "atom_vec.h"
 #include "atom_vec_ellipsoid.h"
 #include "atom_vec_line.h"
 #include "atom_vec_tri.h"
-#include "force.h"
 #include "molecule.h"
 #include "group.h"
 #include "comm.h"
diff --git a/src/read_data.h b/src/read_data.h
index 26ab6ff381..98de607f6b 100644
--- a/src/read_data.h
+++ b/src/read_data.h
@@ -20,7 +20,6 @@ CommandStyle(read_data,ReadData)
 #ifndef LMP_READ_DATA_H
 #define LMP_READ_DATA_H
 
-#include <cstdio>
 #include "pointers.h"
 
 namespace LAMMPS_NS {
diff --git a/src/read_dump.cpp b/src/read_dump.cpp
index 85e2312a42..7316a2f5cd 100644
--- a/src/read_dump.cpp
+++ b/src/read_dump.cpp
@@ -19,25 +19,19 @@
 // due to OpenMPI bug which sets INT64_MAX via its mpi.h
 //   before lmptype.h can set flags to insure it is done correctly
 
-#include "lmptype.h"
+#include "read_dump.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdlib>
-#include "read_dump.h"
+#include <string>
 #include "reader.h"
 #include "style_reader.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "update.h"
-#include "modify.h"
-#include "fix.h"
-#include "compute.h"
 #include "domain.h"
 #include "comm.h"
 #include "force.h"
 #include "irregular.h"
-#include "input.h"
-#include "variable.h"
 #include "error.h"
 #include "memory.h"
 #include "utils.h"
diff --git a/src/read_dump.h b/src/read_dump.h
index 3ee13f779c..66c05cc445 100644
--- a/src/read_dump.h
+++ b/src/read_dump.h
@@ -22,8 +22,6 @@ CommandStyle(read_dump,ReadDump)
 #ifndef LMP_READ_DUMP_H
 #define LMP_READ_DUMP_H
 
-#include <mpi.h>
-#include <cstdio>
 #include "pointers.h"
 
 namespace LAMMPS_NS {
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index 6e156da837..3d2e2b6592 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -11,11 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "read_restart.h"
 #include <mpi.h>
 #include <cstring>
-#include <cstdlib>
 #include <dirent.h>
-#include "read_restart.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "domain.h"
@@ -23,7 +22,6 @@
 #include "irregular.h"
 #include "update.h"
 #include "modify.h"
-#include "fix.h"
 #include "fix_read_restart.h"
 #include "group.h"
 #include "force.h"
diff --git a/src/read_restart.h b/src/read_restart.h
index 23d6ec3fba..63adf37b22 100644
--- a/src/read_restart.h
+++ b/src/read_restart.h
@@ -20,7 +20,6 @@ CommandStyle(read_restart,ReadRestart)
 #ifndef LMP_READ_RESTART_H
 #define LMP_READ_RESTART_H
 
-#include <cstdio>
 #include "pointers.h"
 
 namespace LAMMPS_NS {
diff --git a/src/reader.cpp b/src/reader.cpp
index 5292c9c992..ee032dc822 100644
--- a/src/reader.cpp
+++ b/src/reader.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdio>
-#include <cstring>
 #include "reader.h"
+#include <cstring>
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/reader_native.cpp b/src/reader_native.cpp
index 60b7ecd764..fba613bdd3 100644
--- a/src/reader_native.cpp
+++ b/src/reader_native.cpp
@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "reader_native.h"
 #include <cstring>
 #include <cstdlib>
-#include "reader_native.h"
 #include "atom.h"
 #include "memory.h"
 #include "error.h"
diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp
index 19f0ff2135..a5209956b9 100644
--- a/src/reader_xyz.cpp
+++ b/src/reader_xyz.cpp
@@ -15,10 +15,8 @@
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "reader_xyz.h"
-#include "atom.h"
+#include <cstdlib>
 #include "memory.h"
 #include "error.h"
 #include "force.h"
diff --git a/src/region.cpp b/src/region.cpp
index 6b49a2819b..7a676de1af 100644
--- a/src/region.cpp
+++ b/src/region.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "region.h"
+#include <cmath>
+#include <cstring>
 #include "update.h"
 #include "domain.h"
 #include "lattice.h"
diff --git a/src/region.h b/src/region.h
index 6a3806fed7..0dce004a5b 100644
--- a/src/region.h
+++ b/src/region.h
@@ -14,7 +14,7 @@
 #ifndef LMP_REGION_H
 #define LMP_REGION_H
 
-#include "pointers.h"
+#include "pointers.h"  // IWYU pragma: export
 
 namespace LAMMPS_NS {
 
diff --git a/src/region_block.cpp b/src/region_block.cpp
index e55c481189..8ea8b3f202 100644
--- a/src/region_block.cpp
+++ b/src/region_block.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "region_block.h"
+#include <cstring>
 #include "force.h"
 #include "domain.h"
 #include "math_extra.h"
diff --git a/src/region_cone.cpp b/src/region_cone.cpp
index 72f56a268f..3c7d0a29d8 100644
--- a/src/region_cone.cpp
+++ b/src/region_cone.cpp
@@ -15,10 +15,9 @@
    Contributing author: Pim Schravendijk
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "region_cone.h"
+#include <cmath>
+#include <cstring>
 #include "domain.h"
 #include "error.h"
 #include "force.h"
diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp
index 7709c57aab..b2c06270d0 100644
--- a/src/region_cylinder.cpp
+++ b/src/region_cylinder.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "region_cylinder.h"
+#include <cmath>
+#include <cstring>
 #include "update.h"
 #include "domain.h"
 #include "input.h"
diff --git a/src/region_deprecated.cpp b/src/region_deprecated.cpp
index 87225959fa..a2e4e88393 100644
--- a/src/region_deprecated.cpp
+++ b/src/region_deprecated.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "region_deprecated.h"
+#include <cstring>
 #include "comm.h"
 #include "error.h"
 
diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp
index 96d3bed16c..fe074a6b4c 100644
--- a/src/region_intersect.cpp
+++ b/src/region_intersect.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "region_intersect.h"
+#include <cstring>
 #include "domain.h"
 #include "error.h"
 #include "force.h"
diff --git a/src/region_plane.cpp b/src/region_plane.cpp
index e67a2c85bd..85671357ef 100644
--- a/src/region_plane.cpp
+++ b/src/region_plane.cpp
@@ -11,10 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "region_plane.h"
+#include <cmath>
 #include "error.h"
 #include "force.h"
 
diff --git a/src/region_prism.cpp b/src/region_prism.cpp
index 22fc504c37..b6c54c2fb9 100644
--- a/src/region_prism.cpp
+++ b/src/region_prism.cpp
@@ -15,10 +15,8 @@
    Contributing author: Pieter in 't Veld (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "region_prism.h"
+#include <cstring>
 #include "domain.h"
 #include "force.h"
 #include "math_extra.h"
diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp
index 8080ef5882..bf874ad311 100644
--- a/src/region_sphere.cpp
+++ b/src/region_sphere.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
 #include "region_sphere.h"
+#include <cmath>
+#include <cstring>
 #include "update.h"
 #include "input.h"
 #include "variable.h"
diff --git a/src/region_union.cpp b/src/region_union.cpp
index 33ac6fedd7..be1fe6eeff 100644
--- a/src/region_union.cpp
+++ b/src/region_union.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "region_union.h"
+#include <cstring>
 #include "domain.h"
 #include "error.h"
 #include "force.h"
diff --git a/src/replicate.cpp b/src/replicate.cpp
index 3c8f4a8aee..1617ab0313 100644
--- a/src/replicate.cpp
+++ b/src/replicate.cpp
@@ -11,12 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "replicate.h"
+#include <mpi.h>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec.h"
-#include "atom_vec_hybrid.h"
 #include "force.h"
 #include "domain.h"
 #include "comm.h"
diff --git a/src/rerun.cpp b/src/rerun.cpp
index 063ea882c2..3cd1c53628 100644
--- a/src/rerun.cpp
+++ b/src/rerun.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "rerun.h"
+#include <cstring>
 #include "read_dump.h"
 #include "domain.h"
 #include "update.h"
diff --git a/src/reset_ids.cpp b/src/reset_ids.cpp
index b2cf7a9bbc..857738e841 100644
--- a/src/reset_ids.cpp
+++ b/src/reset_ids.cpp
@@ -12,6 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "reset_ids.h"
+#include <mpi.h>
 #include "atom.h"
 #include "atom_vec.h"
 #include "domain.h"
@@ -28,7 +29,7 @@ ResetIDs::ResetIDs(LAMMPS *lmp) : Pointers(lmp) {}
 
 /* ---------------------------------------------------------------------- */
 
-void ResetIDs::command(int narg, char **/*arg*/)
+void ResetIDs::command(int narg, char ** /* arg */)
 {
   if (domain->box_exist == 0)
     error->all(FLERR,"Reset_ids command before simulation box is defined");
diff --git a/src/respa.cpp b/src/respa.cpp
index 6fa9959d78..a184756335 100644
--- a/src/respa.cpp
+++ b/src/respa.cpp
@@ -15,14 +15,14 @@
    Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "respa.h"
+#include <cstring>
 #include "neighbor.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "domain.h"
 #include "comm.h"
+#include "fix.h"
 #include "force.h"
 #include "pair.h"
 #include "bond.h"
@@ -33,10 +33,8 @@
 #include "output.h"
 #include "update.h"
 #include "modify.h"
-#include "compute.h"
 #include "fix_respa.h"
 #include "timer.h"
-#include "memory.h"
 #include "error.h"
 #include "utils.h"
 #include "pair_hybrid.h"
diff --git a/src/run.cpp b/src/run.cpp
index beb71be52c..2c2f00a7a8 100644
--- a/src/run.cpp
+++ b/src/run.cpp
@@ -11,9 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstdlib>
-#include <cstring>
 #include "run.h"
+#include <cstring>
 #include "domain.h"
 #include "update.h"
 #include "force.h"
diff --git a/src/set.cpp b/src/set.cpp
index 00b2d8a9b0..3bf00063c5 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -11,11 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "set.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "set.h"
+#include <climits>
 #include "atom.h"
 #include "atom_vec.h"
 #include "atom_vec_ellipsoid.h"
@@ -26,9 +26,7 @@
 #include "region.h"
 #include "group.h"
 #include "comm.h"
-#include "neighbor.h"
 #include "force.h"
-#include "pair.h"
 #include "input.h"
 #include "variable.h"
 #include "random_park.h"
diff --git a/src/special.cpp b/src/special.cpp
index 903794c0f6..3dd817bc7f 100644
--- a/src/special.cpp
+++ b/src/special.cpp
@@ -11,19 +11,17 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cstdio>
 #include "special.h"
+#include <mpi.h>
 #include "atom.h"
 #include "atom_vec.h"
 #include "force.h"
 #include "comm.h"
 #include "modify.h"
 #include "fix.h"
-#include "accelerator_kokkos.h"
+#include "accelerator_kokkos.h"  // IWYU pragma: export
 #include "atom_masks.h"
 #include "memory.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/thermo.cpp b/src/thermo.cpp
index bba867d195..3748ee77fe 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -15,12 +15,10 @@
 // due to OpenMPI bug which sets INT64_MAX via its mpi.h
 //   before lmptype.h can set flags to insure it is done correctly
 
-#include "lmptype.h"
+#include "thermo.h"
 #include <mpi.h>
 #include <cmath>
-#include <cstdlib>
 #include <cstring>
-#include "thermo.h"
 #include "atom.h"
 #include "update.h"
 #include "comm.h"
@@ -43,11 +41,8 @@
 #include "kspace.h"
 #include "output.h"
 #include "timer.h"
-#include "math_const.h"
 #include "memory.h"
 #include "error.h"
-#include "universe.h"
-
 #include "math_const.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/thermo.h b/src/thermo.h
index 8c32f24d3c..f2384e0ac3 100644
--- a/src/thermo.h
+++ b/src/thermo.h
@@ -18,9 +18,6 @@
 
 namespace LAMMPS_NS {
 
-class DumpNetCDF;
-class DumpNetCDFMPIIO;
-
 class Thermo : protected Pointers {
   friend class MinCG;                  // accesses compute_pe
   friend class DumpNetCDF;             // accesses thermo properties
diff --git a/src/timer.cpp b/src/timer.cpp
index 65cb6ab5d8..0a5e56ab35 100644
--- a/src/timer.cpp
+++ b/src/timer.cpp
@@ -11,14 +11,13 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "timer.h"
 #include <mpi.h>
 #include <cstring>
 #include <cstdlib>
-#include "timer.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
-#include "memory.h"
 
 #ifdef _WIN32
 #include <windows.h>
diff --git a/src/universe.cpp b/src/universe.cpp
index dba31f8b76..036b3a7e66 100644
--- a/src/universe.cpp
+++ b/src/universe.cpp
@@ -11,12 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "universe.h"
 #include <mpi.h>
 #include <cctype>
 #include <cstdlib>
 #include <cstring>
-#include <cstdio>
-#include "universe.h"
 #include "version.h"
 #include "error.h"
 #include "force.h"
diff --git a/src/universe.h b/src/universe.h
index 3073409b86..fd6655c749 100644
--- a/src/universe.h
+++ b/src/universe.h
@@ -14,7 +14,6 @@
 #ifndef LMP_UNIVERSE_H
 #define LMP_UNIVERSE_H
 
-#include <cstdio>
 #include "pointers.h"
 
 namespace LAMMPS_NS {
diff --git a/src/update.cpp b/src/update.cpp
index f5e706e354..68a6a1a057 100644
--- a/src/update.cpp
+++ b/src/update.cpp
@@ -11,23 +11,18 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-#include <cstdlib>
 #include "update.h"
+#include <cstring>
 #include "integrate.h"
 #include "min.h"
 #include "style_integrate.h"
 #include "style_minimize.h"
 #include "neighbor.h"
-#include "neigh_list.h"
 #include "force.h"
 #include "modify.h"
 #include "fix.h"
-#include "domain.h"
-#include "region.h"
 #include "compute.h"
 #include "output.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -83,7 +78,7 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
   create_integrate(1,&str,1);
 
   str = (char *) "cg";
-  create_minimize(1,&str);
+  create_minimize(1,&str,1);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -381,22 +376,69 @@ Integrate *Update::integrate_creator(LAMMPS *lmp, int narg, char ** arg)
 
 /* ---------------------------------------------------------------------- */
 
-void Update::create_minimize(int narg, char **arg)
+void Update::create_minimize(int narg, char **arg, int trysuffix)
 {
-  if (narg != 1) error->all(FLERR,"Illegal min_style command");
+  if (narg < 1) error->all(FLERR,"Illegal run_style command");
 
   delete [] minimize_style;
   delete minimize;
 
-  if (minimize_map->find(arg[0]) != minimize_map->end()) {
-    MinimizeCreator minimize_creator = (*minimize_map)[arg[0]];
-    minimize = minimize_creator(lmp);
-  }
-  else error->all(FLERR,"Illegal min_style command");
+  int sflag;
+  new_minimize(arg[0],narg-1,&arg[1],trysuffix,sflag);
 
-  int n = strlen(arg[0]) + 1;
-  minimize_style = new char[n];
-  strcpy(minimize_style,arg[0]);
+  if (sflag) {
+    char estyle[256];
+    if (sflag == 1) snprintf(estyle,256,"%s/%s",arg[0],lmp->suffix);
+    else snprintf(estyle,256,"%s/%s",arg[0],lmp->suffix2);
+    int n = strlen(estyle) + 1;
+    minimize_style = new char[n];
+    strcpy(minimize_style,estyle);
+  } else {
+    int n = strlen(arg[0]) + 1;
+    minimize_style = new char[n];
+    strcpy(minimize_style,arg[0]);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   create the Minimize style, first with suffix appended
+------------------------------------------------------------------------- */
+
+void Update::new_minimize(char *style, int narg, char **arg,
+                           int trysuffix, int &sflag)
+{
+  if (trysuffix && lmp->suffix_enable) {
+    if (lmp->suffix) {
+      sflag = 1;
+      char estyle[256];
+      snprintf(estyle,256,"%s/%s",style,lmp->suffix);
+      if (minimize_map->find(estyle) != minimize_map->end()) {
+        MinimizeCreator minimize_creator = (*minimize_map)[estyle];
+        minimize = minimize_creator(lmp);
+        return;
+      }
+    }
+
+    if (lmp->suffix2) {
+      sflag = 2;
+      char estyle[256];
+      snprintf(estyle,256,"%s/%s",style,lmp->suffix2);
+      if (minimize_map->find(estyle) != minimize_map->end()) {
+        MinimizeCreator minimize_creator = (*minimize_map)[estyle];
+        minimize = minimize_creator(lmp);
+        return;
+      }
+    }
+  }
+
+  sflag = 0;
+  if (minimize_map->find(style) != minimize_map->end()) {
+    MinimizeCreator minimize_creator = (*minimize_map)[style];
+    minimize = minimize_creator(lmp);
+    return;
+  }
+
+  error->all(FLERR,"Illegal minimize style");
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/update.h b/src/update.h
index d3602ef21e..e70325a498 100644
--- a/src/update.h
+++ b/src/update.h
@@ -63,7 +63,7 @@ class Update : protected Pointers {
   void init();
   void set_units(const char *);
   void create_integrate(int, char **, int);
-  void create_minimize(int, char **);
+  void create_minimize(int, char **, int);
   void reset_timestep(int, char **);
   void reset_timestep(bigint);
   void update_time();
@@ -71,6 +71,7 @@ class Update : protected Pointers {
 
  private:
   void new_integrate(char *, int, char **, int, int &);
+  void new_minimize(char *, int, char **, int, int &);
 
   template <typename T> static Integrate *integrate_creator(LAMMPS *, int, char **);
   template <typename T> static Min *minimize_creator(LAMMPS *);
diff --git a/src/utils.cpp b/src/utils.cpp
index 4e39187f77..5e53a3a09d 100644
--- a/src/utils.cpp
+++ b/src/utils.cpp
@@ -11,10 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
+#include "utils.h"
 #include <cstring>
 #include <cstdlib>
-#include "utils.h"
 #include "lammps.h"
 #include "error.h"
 
diff --git a/src/variable.cpp b/src/variable.cpp
index 63a425bcf5..1093ce9066 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -11,12 +11,14 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "variable.h"
+#include <mpi.h>
 #include <cmath>
 #include <cstdlib>
 #include <cstring>
 #include <cctype>
 #include <unistd.h>
-#include "variable.h"
+#include <string>
 #include "universe.h"
 #include "atom.h"
 #include "update.h"
@@ -26,6 +28,7 @@
 #include "region.h"
 #include "modify.h"
 #include "compute.h"
+#include "input.h"
 #include "fix.h"
 #include "fix_store.h"
 #include "force.h"
@@ -33,7 +36,6 @@
 #include "thermo.h"
 #include "random_mars.h"
 #include "math_const.h"
-#include "atom_masks.h"
 #include "lmppython.h"
 #include "memory.h"
 #include "info.h"
@@ -1301,8 +1303,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
         if (word[0] == 'C') lowercase = 0;
 
         int icompute = modify->find_compute(word+2);
-        if (icompute < 0)
-          print_var_error(FLERR,"Invalid compute ID in variable formula",ivar);
+        if (icompute < 0) {
+          std::string mesg = "Invalid compute ID '";
+          mesg += (word+2);
+          mesg += "' in variable formula";
+          print_var_error(FLERR,mesg.c_str(),ivar);
+        }
         Compute *compute = modify->compute[icompute];
 
         // parse zero or one or two trailing brackets
@@ -1603,9 +1609,10 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
 
         int ifix = modify->find_fix(word+2);
         if (ifix < 0) {
-          char msg[128];
-          snprintf(msg,128,"Invalid fix ID '%s' in variable formula",word+2);
-          print_var_error(FLERR,msg,ivar);
+          std::string mesg = "Invalid fix ID '";
+          mesg += (word+2);
+          mesg += "' in variable formula";
+          print_var_error(FLERR,mesg.c_str(),ivar);
         }
         Fix *fix = modify->fix[ifix];
 
@@ -3791,8 +3798,12 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
   // group to operate on
 
   int igroup = group->find(args[0]);
-  if (igroup == -1)
-    print_var_error(FLERR,"Group ID in variable formula does not exist",ivar);
+  if (igroup == -1) {
+    std::string mesg = "Group ID '";
+    mesg += args[0];
+    mesg += "' in variable formula does not exist";
+    print_var_error(FLERR,mesg.c_str(),ivar);
+  }
 
   // match word to group function
 
@@ -4000,8 +4011,12 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
 int Variable::region_function(char *id, int ivar)
 {
   int iregion = domain->find_region(id);
-  if (iregion == -1)
-    print_var_error(FLERR,"Region ID in variable formula does not exist",ivar);
+  if (iregion == -1) {
+    std::string mesg = "Region ID '";
+    mesg += id;
+    mesg += "' in variable formula does not exist";
+    print_var_error(FLERR,mesg.c_str(),ivar);
+  }
 
   // init region in case sub-regions have been deleted
 
@@ -4079,9 +4094,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
 
       int icompute = modify->find_compute(&args[0][2]);
       if (icompute < 0) {
-        char msg[128];
-        snprintf(msg,128,"Invalid compute ID '%s' in variable formula",word+2);
-        print_var_error(FLERR,msg,ivar);
+        std::string mesg = "Invalid compute ID '";
+        mesg += (args[0]+2);
+        mesg += "' in variable formula";
+        print_var_error(FLERR,mesg.c_str(),ivar);
       }
       compute = modify->compute[icompute];
       if (index == 0 && compute->vector_flag) {
@@ -4122,13 +4138,20 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
       } else index = 0;
 
       int ifix = modify->find_fix(&args[0][2]);
-      if (ifix < 0)
-        print_var_error(FLERR,"Invalid fix ID in variable formula",ivar);
+      if (ifix < 0) {
+        std::string mesg = "Invalid fix ID '";
+        mesg += (args[0]+2);
+        mesg += "' in variable formula";
+        print_var_error(FLERR,mesg.c_str(),ivar);
+      }
       fix = modify->fix[ifix];
       if (index == 0 && fix->vector_flag) {
-        if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
-          print_var_error(FLERR,"Fix in variable not computed at "
-                          "compatible time",ivar);
+        if (update->whichflag > 0 && update->ntimestep % fix->global_freq) {
+          std::string mesg = "Fix with ID '";
+          mesg += (args[0]+2);
+          mesg += "' in variable formula not computed at compatible time";
+          print_var_error(FLERR,mesg.c_str(),ivar);
+        }
         nvec = fix->size_vector;
         nstride = 1;
       } else if (index && fix->array_flag) {
@@ -4335,9 +4358,12 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
       print_var_error(FLERR,"Invalid special function in variable formula",ivar);
 
     int ivar = find(args[0]);
-    if (ivar < 0)
-      print_var_error(FLERR,"Variable ID in "
-                      "variable formula does not exist",ivar);
+    if (ivar < 0) {
+      std::string mesg = "Variable ID '";
+      mesg += args[0];
+      mesg += "' in variable formula does not exist";
+      print_var_error(FLERR,mesg.c_str(),ivar);
+    }
 
     // SCALARFILE has single current value, read next one
     // save value in tree or on argstack
diff --git a/src/variable.h b/src/variable.h
index 512195bd14..a504da14ec 100644
--- a/src/variable.h
+++ b/src/variable.h
@@ -14,9 +14,7 @@
 #ifndef LMP_VARIABLE_H
 #define LMP_VARIABLE_H
 
-#include <cstdlib>
 #include "pointers.h"
-#include "input.h"
 
 namespace LAMMPS_NS {
 
diff --git a/src/velocity.cpp b/src/velocity.cpp
index 95d820cc22..e5985884f8 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -11,14 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <mpi.h>
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "velocity.h"
+#include <cmath>
+#include <cstring>
 #include "atom.h"
-#include "update.h"
 #include "domain.h"
 #include "lattice.h"
 #include "input.h"
diff --git a/src/verlet.cpp b/src/verlet.cpp
index fcba248d5f..8cd6fe940d 100644
--- a/src/verlet.cpp
+++ b/src/verlet.cpp
@@ -11,8 +11,8 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "verlet.h"
+#include <cstring>
 #include "neighbor.h"
 #include "domain.h"
 #include "comm.h"
@@ -28,10 +28,7 @@
 #include "output.h"
 #include "update.h"
 #include "modify.h"
-#include "compute.h"
-#include "fix.h"
 #include "timer.h"
-#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/version.h b/src/version.h
index 8a8cbec57e..7387a3a1a4 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "19 Jul 2019"
+#define LAMMPS_VERSION "7 Aug 2019"
diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp
index 9bf54b3c08..8e5b4fcb71 100644
--- a/src/write_coeff.cpp
+++ b/src/write_coeff.cpp
@@ -11,10 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "write_coeff.h"
 #include <cstring>
 #include <cstdlib>
+#include <cctype>
 #include <unistd.h>
-#include "write_coeff.h"
 #include "pair.h"
 #include "bond.h"
 #include "angle.h"
diff --git a/src/write_coeff.h b/src/write_coeff.h
index 569a615e6e..b995e60d63 100644
--- a/src/write_coeff.h
+++ b/src/write_coeff.h
@@ -20,7 +20,6 @@ CommandStyle(write_coeff,WriteCoeff)
 #ifndef LMP_WRITE_COEFF_H
 #define LMP_WRITE_COEFF_H
 
-#include <cstdio>
 #include "pointers.h"
 
 namespace LAMMPS_NS {
diff --git a/src/write_data.cpp b/src/write_data.cpp
index decc92ea8c..3d788b9665 100644
--- a/src/write_data.cpp
+++ b/src/write_data.cpp
@@ -11,12 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "write_data.h"
 #include <mpi.h>
 #include <cstring>
-#include "write_data.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "group.h"
 #include "force.h"
 #include "pair.h"
 #include "bond.h"
diff --git a/src/write_data.h b/src/write_data.h
index 6f1bb2ec47..1c0f6b2a7c 100644
--- a/src/write_data.h
+++ b/src/write_data.h
@@ -20,7 +20,6 @@ CommandStyle(write_data,WriteData)
 #ifndef LMP_WRITE_DATA_H
 #define LMP_WRITE_DATA_H
 
-#include <cstdio>
 #include "pointers.h"
 
 namespace LAMMPS_NS {
diff --git a/src/write_dump.cpp b/src/write_dump.cpp
index 072680a8a5..31ceb4cbbf 100644
--- a/src/write_dump.cpp
+++ b/src/write_dump.cpp
@@ -15,15 +15,13 @@
    Contributing author:  Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "write_dump.h"
+#include <cstring>
+#include <string>
 #include "style_dump.h"
 #include "dump.h"
 #include "dump_image.h"
-#include "atom.h"
 #include "comm.h"
-#include "group.h"
-#include "input.h"
 #include "update.h"
 #include "error.h"
 #include "utils.h"
diff --git a/src/write_restart.cpp b/src/write_restart.cpp
index e0e17cd292..4b84e790b8 100644
--- a/src/write_restart.cpp
+++ b/src/write_restart.cpp
@@ -11,12 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include "write_restart.h"
 #include <mpi.h>
 #include <cstring>
-#include "write_restart.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "atom_vec_hybrid.h"
 #include "group.h"
 #include "force.h"
 #include "pair.h"
diff --git a/src/write_restart.h b/src/write_restart.h
index c6202acbfd..e7cdc6a501 100644
--- a/src/write_restart.h
+++ b/src/write_restart.h
@@ -20,7 +20,6 @@ CommandStyle(write_restart,WriteRestart)
 #ifndef LMP_WRITE_RESTART_H
 #define LMP_WRITE_RESTART_H
 
-#include <cstdio>
 #include "pointers.h"
 
 namespace LAMMPS_NS {