Merge pull request #3310 from akohlmey/next_patch_release

Update version strings for the next patch release

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/codeql-analysis.yml

@@ -5,12 +5,19 @@ on:
   push:
     branches: [develop]
 
+  workflow_dispatch:
+
 jobs:
   analyze:
     name: Analyze
     if: ${{ github.repository == 'lammps/lammps' }}
     runs-on: ubuntu-latest
 
+    permissions:
+      security-events: write
+      actions: read
+      contents: read
+
     strategy:
       fail-fast: false
       matrix:
@@ -18,17 +25,17 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
     - name: Setup Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
+      uses: github/codeql-action/init@v2
       with:
         languages: ${{ matrix.language }}
         config-file: ./.github/codeql/${{ matrix.language }}.yml
@@ -46,4 +53,4 @@ jobs:
         cmake --build . --parallel 2
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      uses: github/codeql-action/analyze@v2

.github/workflows/compile-msvc.yml

@@ -5,6 +5,8 @@ on:
   push:
     branches: [develop]
 
+  workflow_dispatch:
+
 jobs:
   build:
     name: Windows Compilation Test
@@ -13,12 +15,12 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
     - name: Select Python version
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.10'
 

.github/workflows/unittest-macos.yml

@@ -5,6 +5,8 @@ on:
   push:
     branches: [develop]
 
+  workflow_dispatch:
+
 jobs:
   build:
     name: MacOS Unit Test
@@ -15,7 +17,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
@@ -26,7 +28,7 @@ jobs:
       run: mkdir build
 
     - name: Set up ccache
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ${{ env.CCACHE_DIR }}
         key: macos-ccache-${{ github.sha }}

cmake/CMakeLists.jpeg

@@ -0,0 +1,615 @@
+cmake_minimum_required(VERSION 3.10)
+# When using CMake 3.4 and later, don't export symbols from executables unless
+# the CMAKE_ENABLE_EXPORTS variable is set.
+if(POLICY CMP0065)
+  cmake_policy(SET CMP0065 NEW)
+endif()
+if (POLICY CMP0077)
+  cmake_policy(SET CMP0077 NEW)
+endif()
+if(CMAKE_EXECUTABLE_SUFFIX)
+  set(CMAKE_EXECUTABLE_SUFFIX_TMP ${CMAKE_EXECUTABLE_SUFFIX})
+endif()
+
+project(libjpeg-turbo C)
+set(VERSION 2.1.3)
+set(COPYRIGHT_YEAR "1991-2022")
+string(REPLACE "." ";" VERSION_TRIPLET ${VERSION})
+list(GET VERSION_TRIPLET 0 VERSION_MAJOR)
+list(GET VERSION_TRIPLET 1 VERSION_MINOR)
+list(GET VERSION_TRIPLET 2 VERSION_REVISION)
+function(pad_number NUMBER OUTPUT_LEN)
+  string(LENGTH "${${NUMBER}}" INPUT_LEN)
+  if(INPUT_LEN LESS OUTPUT_LEN)
+    math(EXPR ZEROES "${OUTPUT_LEN} - ${INPUT_LEN} - 1")
+    set(NUM ${${NUMBER}})
+    foreach(C RANGE ${ZEROES})
+      set(NUM "0${NUM}")
+    endforeach()
+    set(${NUMBER} ${NUM} PARENT_SCOPE)
+  endif()
+endfunction()
+pad_number(VERSION_MINOR 3)
+pad_number(VERSION_REVISION 3)
+set(LIBJPEG_TURBO_VERSION_NUMBER ${VERSION_MAJOR}${VERSION_MINOR}${VERSION_REVISION})
+
+# CMake 3.14 and later sets CMAKE_MACOSX_BUNDLE to TRUE by default when
+# CMAKE_SYSTEM_NAME is iOS, tvOS, or watchOS, which breaks the libjpeg-turbo
+# build.  (Specifically, when CMAKE_MACOSX_BUNDLE is TRUE, executables for
+# Apple platforms are built as application bundles, which causes CMake to
+# complain that our install() directives for executables do not specify a
+# BUNDLE DESTINATION.  Even if CMake did not complain, building executables as
+# application bundles would break our iOS packages.)
+set(CMAKE_MACOSX_BUNDLE FALSE)
+
+string(TIMESTAMP DEFAULT_BUILD "%Y%m%d")
+set(BUILD ${DEFAULT_BUILD} CACHE STRING "Build string (default: ${DEFAULT_BUILD})")
+
+# NOTE: On Windows, this does nothing except when using MinGW or Cygwin.
+# CMAKE_BUILD_TYPE has no meaning in Visual Studio, and it always defaults to
+# Debug when using NMake.
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release)
+endif()
+message(STATUS "CMAKE_BUILD_TYPE = ${CMAKE_BUILD_TYPE}")
+
+message(STATUS "VERSION = ${VERSION}, BUILD = ${BUILD}")
+
+include(cmakescripts/PackageInfo.cmake)
+
+# Detect CPU type and whether we're building 64-bit or 32-bit code
+math(EXPR BITS "${CMAKE_SIZEOF_VOID_P} * 8")
+string(TOLOWER ${CMAKE_SYSTEM_PROCESSOR} CMAKE_SYSTEM_PROCESSOR_LC)
+set(COUNT 1)
+foreach(ARCH ${CMAKE_OSX_ARCHITECTURES})
+  if(COUNT GREATER 1)
+    message(FATAL_ERROR "The libjpeg-turbo build system does not support multiple values in CMAKE_OSX_ARCHITECTURES.")
+  endif()
+  math(EXPR COUNT "${COUNT}+1")
+endforeach()
+if(CMAKE_SYSTEM_PROCESSOR_LC MATCHES "x86_64" OR
+  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "amd64" OR
+  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "i[0-9]86" OR
+  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "x86" OR
+  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "ia32")
+  if(BITS EQUAL 64 OR CMAKE_C_COMPILER_ABI MATCHES "ELF X32")
+    set(CPU_TYPE x86_64)
+  else()
+    set(CPU_TYPE i386)
+  endif()
+  if(NOT CMAKE_SYSTEM_PROCESSOR STREQUAL ${CPU_TYPE})
+    set(CMAKE_SYSTEM_PROCESSOR ${CPU_TYPE})
+  endif()
+elseif(CMAKE_SYSTEM_PROCESSOR_LC STREQUAL "aarch64" OR
+  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^arm")
+  if(BITS EQUAL 64)
+    set(CPU_TYPE arm64)
+  else()
+    set(CPU_TYPE arm)
+  endif()
+elseif(CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^ppc" OR
+  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^powerpc")
+  set(CPU_TYPE powerpc)
+else()
+  set(CPU_TYPE ${CMAKE_SYSTEM_PROCESSOR_LC})
+endif()
+if(CMAKE_OSX_ARCHITECTURES MATCHES "x86_64" OR
+  CMAKE_OSX_ARCHITECTURES MATCHES "arm64" OR
+  CMAKE_OSX_ARCHITECTURES MATCHES "i386")
+  set(CPU_TYPE ${CMAKE_OSX_ARCHITECTURES})
+endif()
+if(CMAKE_OSX_ARCHITECTURES MATCHES "ppc")
+  set(CPU_TYPE powerpc)
+endif()
+if(MSVC_IDE AND CMAKE_GENERATOR_PLATFORM MATCHES "arm64")
+  set(CPU_TYPE arm64)
+endif()
+
+message(STATUS "${BITS}-bit build (${CPU_TYPE})")
+
+macro(report_directory var)
+  if(CMAKE_INSTALL_${var} STREQUAL CMAKE_INSTALL_FULL_${var})
+    message(STATUS "CMAKE_INSTALL_${var} = ${CMAKE_INSTALL_${var}}")
+  else()
+    message(STATUS "CMAKE_INSTALL_${var} = ${CMAKE_INSTALL_${var}} (${CMAKE_INSTALL_FULL_${var}})")
+  endif()
+  mark_as_advanced(CLEAR CMAKE_INSTALL_${var})
+endmacro()
+
+set(DIRLIST "BINDIR;DATAROOTDIR;DOCDIR;INCLUDEDIR;LIBDIR")
+if(UNIX)
+  list(APPEND DIRLIST "MANDIR")
+endif()
+foreach(dir ${DIRLIST})
+  report_directory(${dir})
+endforeach()
+
+
+###############################################################################
+# CONFIGURATION OPTIONS
+###############################################################################
+
+macro(boolean_number var)
+  if(${var})
+    set(${var} 1 ${ARGN})
+  else()
+    set(${var} 0 ${ARGN})
+  endif()
+endmacro()
+
+option(ENABLE_SHARED "Build shared libraries" FALSE)
+boolean_number(ENABLE_SHARED)
+option(ENABLE_STATIC "Build static libraries" TRUE)
+boolean_number(ENABLE_STATIC)
+option(REQUIRE_SIMD "Generate a fatal error if SIMD extensions are not available for this platform (default is to fall back to a non-SIMD build)" FALSE)
+boolean_number(REQUIRE_SIMD)
+option(WITH_12BIT "Encode/decode JPEG images with 12-bit samples (implies WITH_ARITH_DEC=0 WITH_ARITH_ENC=0 WITH_JAVA=0 WITH_SIMD=0 WITH_TURBOJPEG=0 )" FALSE)
+boolean_number(WITH_12BIT)
+option(WITH_ARITH_DEC "Include arithmetic decoding support when emulating the libjpeg v6b API/ABI" TRUE)
+boolean_number(WITH_ARITH_DEC)
+option(WITH_ARITH_ENC "Include arithmetic encoding support when emulating the libjpeg v6b API/ABI" TRUE)
+boolean_number(WITH_ARITH_ENC)
+if(CMAKE_C_COMPILER_ABI MATCHES "ELF X32")
+  set(WITH_JAVA 0)
+else()
+  option(WITH_JAVA "Build Java wrapper for the TurboJPEG API library (implies ENABLE_SHARED=1)" FALSE)
+  boolean_number(WITH_JAVA)
+endif()
+option(WITH_JPEG7 "Emulate libjpeg v7 API/ABI (this makes ${CMAKE_PROJECT_NAME} backward-incompatible with libjpeg v6b)" FALSE)
+boolean_number(WITH_JPEG7)
+option(WITH_JPEG8 "Emulate libjpeg v8 API/ABI (this makes ${CMAKE_PROJECT_NAME} backward-incompatible with libjpeg v6b)" FALSE)
+boolean_number(WITH_JPEG8)
+option(WITH_MEM_SRCDST "Include in-memory source/destination manager functions when emulating the libjpeg v6b or v7 API/ABI" TRUE)
+boolean_number(WITH_MEM_SRCDST)
+option(WITH_SIMD "Include SIMD extensions, if available for this platform" FALSE)
+boolean_number(WITH_SIMD)
+option(WITH_TURBOJPEG "Include the TurboJPEG API library and associated test programs" FALSE)
+boolean_number(WITH_TURBOJPEG)
+option(WITH_FUZZ "Build fuzz targets" FALSE)
+
+macro(report_option var desc)
+  if(${var})
+    message(STATUS "${desc} enabled (${var} = ${${var}})")
+  else()
+    message(STATUS "${desc} disabled (${var} = ${${var}})")
+  endif()
+endmacro()
+
+if(WITH_JAVA)
+  set(ENABLE_SHARED 1)
+endif()
+
+# Explicitly setting CMAKE_POSITION_INDEPENDENT_CODE=FALSE disables PIC for all
+# targets, which will cause the shared library builds to fail.  Thus, if shared
+# libraries are enabled and CMAKE_POSITION_INDEPENDENT_CODE is explicitly set
+# to FALSE, we need to unset it, thus restoring the default behavior
+# (automatically using PIC for shared library targets.)
+if(DEFINED CMAKE_POSITION_INDEPENDENT_CODE AND
+  NOT CMAKE_POSITION_INDEPENDENT_CODE AND ENABLE_SHARED)
+  unset(CMAKE_POSITION_INDEPENDENT_CODE CACHE)
+endif()
+
+report_option(ENABLE_SHARED "Shared libraries")
+report_option(ENABLE_STATIC "Static libraries")
+
+if(ENABLE_SHARED)
+  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
+endif()
+
+if(WITH_JPEG8 OR WITH_JPEG7)
+  set(WITH_ARITH_ENC 1)
+  set(WITH_ARITH_DEC 1)
+endif()
+if(WITH_JPEG8)
+  set(WITH_MEM_SRCDST 0)
+endif()
+
+if(WITH_12BIT)
+  set(WITH_ARITH_DEC 0)
+  set(WITH_ARITH_ENC 0)
+  set(WITH_JAVA 0)
+  set(WITH_SIMD 0)
+  set(WITH_TURBOJPEG 0)
+  set(BITS_IN_JSAMPLE 12)
+else()
+  set(BITS_IN_JSAMPLE 8)
+endif()
+report_option(WITH_12BIT "12-bit JPEG support")
+
+if(WITH_ARITH_DEC)
+  set(D_ARITH_CODING_SUPPORTED 1)
+endif()
+if(NOT WITH_12BIT)
+  report_option(WITH_ARITH_DEC "Arithmetic decoding support")
+endif()
+
+if(WITH_ARITH_ENC)
+  set(C_ARITH_CODING_SUPPORTED 1)
+endif()
+if(NOT WITH_12BIT)
+  report_option(WITH_ARITH_ENC "Arithmetic encoding support")
+endif()
+
+if(NOT WITH_12BIT)
+  report_option(WITH_TURBOJPEG "TurboJPEG API library")
+  report_option(WITH_JAVA "TurboJPEG Java wrapper")
+endif()
+
+if(WITH_MEM_SRCDST)
+  set(MEM_SRCDST_SUPPORTED 1)
+  set(MEM_SRCDST_FUNCTIONS "global:  jpeg_mem_dest;  jpeg_mem_src;")
+endif()
+if(NOT WITH_JPEG8)
+  report_option(WITH_MEM_SRCDST "In-memory source/destination managers")
+endif()
+
+set(SO_AGE 2)
+if(WITH_MEM_SRCDST)
+  set(SO_AGE 3)
+endif()
+
+if(WITH_JPEG8)
+  set(JPEG_LIB_VERSION 80)
+elseif(WITH_JPEG7)
+  set(JPEG_LIB_VERSION 70)
+else()
+  set(JPEG_LIB_VERSION 62)
+endif()
+
+math(EXPR JPEG_LIB_VERSION_DIV10 "${JPEG_LIB_VERSION} / 10")
+math(EXPR JPEG_LIB_VERSION_MOD10 "${JPEG_LIB_VERSION} % 10")
+if(JPEG_LIB_VERSION STREQUAL "62")
+  set(DEFAULT_SO_MAJOR_VERSION ${JPEG_LIB_VERSION})
+else()
+  set(DEFAULT_SO_MAJOR_VERSION ${JPEG_LIB_VERSION_DIV10})
+endif()
+if(JPEG_LIB_VERSION STREQUAL "80")
+  set(DEFAULT_SO_MINOR_VERSION 2)
+else()
+  set(DEFAULT_SO_MINOR_VERSION 0)
+endif()
+
+# This causes SO_MAJOR_VERSION/SO_MINOR_VERSION to reset to defaults if
+# WITH_JPEG7 or WITH_JPEG8 has changed.
+if((DEFINED WITH_JPEG7_INT AND NOT WITH_JPEG7 EQUAL WITH_JPEG7_INT) OR
+  (DEFINED WITH_JPEG8_INT AND NOT WITH_JPEG8 EQUAL WITH_JPEG8_INT))
+  set(FORCE_SO_VERSION "FORCE")
+endif()
+set(WITH_JPEG7_INT ${WITH_JPEG7} CACHE INTERNAL "")
+set(WITH_JPEG8_INT ${WITH_JPEG8} CACHE INTERNAL "")
+
+set(SO_MAJOR_VERSION ${DEFAULT_SO_MAJOR_VERSION} CACHE STRING
+  "Major version of the libjpeg API shared library (default: ${DEFAULT_SO_MAJOR_VERSION})"
+  ${FORCE_SO_VERSION})
+set(SO_MINOR_VERSION ${DEFAULT_SO_MINOR_VERSION} CACHE STRING
+  "Minor version of the libjpeg API shared library (default: ${DEFAULT_SO_MINOR_VERSION})"
+  ${FORCE_SO_VERSION})
+
+set(JPEG_LIB_VERSION_DECIMAL "${JPEG_LIB_VERSION_DIV10}.${JPEG_LIB_VERSION_MOD10}")
+message(STATUS "Emulating libjpeg API/ABI v${JPEG_LIB_VERSION_DECIMAL} (WITH_JPEG7 = ${WITH_JPEG7}, WITH_JPEG8 = ${WITH_JPEG8})")
+message(STATUS "libjpeg API shared library version = ${SO_MAJOR_VERSION}.${SO_AGE}.${SO_MINOR_VERSION}")
+
+# Because the TurboJPEG API library uses versioned symbols and changes the
+# names of functions whenever they are modified in a backward-incompatible
+# manner, it is always backward-ABI-compatible with itself, so the major and
+# minor SO versions don't change.  However, we increase the middle number (the
+# SO "age") whenever functions are added to the API.
+set(TURBOJPEG_SO_MAJOR_VERSION 0)
+set(TURBOJPEG_SO_AGE 2)
+set(TURBOJPEG_SO_VERSION 0.${TURBOJPEG_SO_AGE}.0)
+
+
+###############################################################################
+# COMPILER SETTINGS
+###############################################################################
+
+if(MSVC)
+  option(WITH_CRT_DLL
+    "Link all ${CMAKE_PROJECT_NAME} libraries and executables with the C run-time DLL (msvcr*.dll) instead of the static C run-time library (libcmt*.lib.)  The default is to use the C run-time DLL only with the libraries and executables that need it."
+    FALSE)
+  if(NOT WITH_CRT_DLL)
+    # Use the static C library for all build types
+    foreach(var CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
+      CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
+      if(${var} MATCHES "/MD")
+        string(REGEX REPLACE "/MD" "/MT" ${var} "${${var}}")
+      endif()
+    endforeach()
+  endif()
+  add_definitions(-D_CRT_NONSTDC_NO_WARNINGS)
+endif()
+
+if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_C_COMPILER_ID STREQUAL "Clang")
+  # Use the maximum optimization level for release builds
+  foreach(var CMAKE_C_FLAGS_RELEASE CMAKE_C_FLAGS_RELWITHDEBINFO)
+    if(${var} MATCHES "-O2")
+      string(REGEX REPLACE "-O2" "-O3" ${var} "${${var}}")
+    endif()
+  endforeach()
+endif()
+
+if(CMAKE_SYSTEM_NAME STREQUAL "SunOS")
+  if(CMAKE_C_COMPILER_ID MATCHES "SunPro")
+    # Use the maximum optimization level for release builds
+    foreach(var CMAKE_C_FLAGS_RELEASE CMAKE_C_FLAGS_RELWITHDEBINFO)
+      if(${var} MATCHES "-xO3")
+        string(REGEX REPLACE "-xO3" "-xO5" ${var} "${${var}}")
+      endif()
+      if(${var} MATCHES "-xO2")
+        string(REGEX REPLACE "-xO2" "-xO5" ${var} "${${var}}")
+      endif()
+    endforeach()
+  endif()
+endif()
+
+string(TOUPPER ${CMAKE_BUILD_TYPE} CMAKE_BUILD_TYPE_UC)
+
+set(EFFECTIVE_C_FLAGS "${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE_UC}}")
+message(STATUS "Compiler flags = ${EFFECTIVE_C_FLAGS}")
+
+set(EFFECTIVE_LD_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS_${CMAKE_BUILD_TYPE_UC}}")
+message(STATUS "Linker flags = ${EFFECTIVE_LD_FLAGS}")
+
+include(CheckCSourceCompiles)
+include(CheckIncludeFiles)
+include(CheckTypeSize)
+
+check_type_size("size_t" SIZE_T)
+check_type_size("unsigned long" UNSIGNED_LONG)
+
+if(SIZE_T EQUAL UNSIGNED_LONG)
+  check_c_source_compiles("int main(int argc, char **argv) { unsigned long a = argc;  return __builtin_ctzl(a); }"
+    HAVE_BUILTIN_CTZL)
+endif()
+if(MSVC)
+  check_include_files("intrin.h" HAVE_INTRIN_H)
+endif()
+
+if(UNIX)
+  if(CMAKE_CROSSCOMPILING)
+    set(RIGHT_SHIFT_IS_UNSIGNED 0)
+  else()
+    include(CheckCSourceRuns)
+    check_c_source_runs("
+      #include <stdio.h>
+      #include <stdlib.h>
+      int is_shifting_signed (long arg) {
+        long res = arg >> 4;
+        if (res == -0x7F7E80CL)
+          return 1; /* right shift is signed */
+        /* see if unsigned-shift hack will fix it. */
+        /* we can't just test exact value since it depends on width of long... */
+        res |= (~0L) << (32-4);
+        if (res == -0x7F7E80CL)
+          return 0; /* right shift is unsigned */
+        printf(\"Right shift isn't acting as I expect it to.\\\\n\");
+        printf(\"I fear the JPEG software will not work at all.\\\\n\\\\n\");
+        return 0; /* try it with unsigned anyway */
+      }
+      int main (void) {
+        exit(is_shifting_signed(-0x7F7E80B1L));
+      }" RIGHT_SHIFT_IS_UNSIGNED)
+  endif()
+endif()
+
+if(MSVC)
+  set(INLINE_OPTIONS "__inline;inline")
+else()
+  set(INLINE_OPTIONS "__inline__;inline")
+endif()
+option(FORCE_INLINE "Force function inlining" TRUE)
+boolean_number(FORCE_INLINE)
+if(FORCE_INLINE)
+  if(MSVC)
+    list(INSERT INLINE_OPTIONS 0 "__forceinline")
+  else()
+    list(INSERT INLINE_OPTIONS 0 "inline __attribute__((always_inline))")
+    list(INSERT INLINE_OPTIONS 0 "__inline__ __attribute__((always_inline))")
+  endif()
+endif()
+foreach(inline ${INLINE_OPTIONS})
+  check_c_source_compiles("${inline} static int foo(void) { return 0; } int main(void) { return foo(); }"
+    INLINE_WORKS)
+  if(INLINE_WORKS)
+    set(INLINE ${inline})
+    break()
+  endif()
+endforeach()
+if(NOT INLINE_WORKS)
+  message(FATAL_ERROR "Could not determine how to inline functions.")
+endif()
+message(STATUS "INLINE = ${INLINE} (FORCE_INLINE = ${FORCE_INLINE})")
+
+if(WITH_TURBOJPEG)
+  if(MSVC)
+    set(THREAD_LOCAL "__declspec(thread)")
+  else()
+    set(THREAD_LOCAL "__thread")
+  endif()
+  check_c_source_compiles("${THREAD_LOCAL} int i;  int main(void) { i = 0;  return i; }" HAVE_THREAD_LOCAL)
+  if(HAVE_THREAD_LOCAL)
+    message(STATUS "THREAD_LOCAL = ${THREAD_LOCAL}")
+  else()
+    message(WARNING "Thread-local storage is not available.  The TurboJPEG API library's global error handler will not be thread-safe.")
+    unset(THREAD_LOCAL)
+  endif()
+endif()
+
+if(UNIX AND NOT APPLE)
+  file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map "VERS_1 { global: *; };")
+  set(CMAKE_REQUIRED_FLAGS
+    "-Wl,--version-script,${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
+  check_c_source_compiles("int main(void) { return 0; }" HAVE_VERSION_SCRIPT)
+  set(CMAKE_REQUIRED_FLAGS)
+  file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map)
+  if(HAVE_VERSION_SCRIPT)
+    message(STATUS "Linker supports GNU-style version scripts")
+    set(MAPFLAG "-Wl,--version-script,")
+    set(TJMAPFLAG "-Wl,--version-script,")
+  else()
+    message(STATUS "Linker does not support GNU-style version scripts")
+    if(CMAKE_SYSTEM_NAME STREQUAL "SunOS")
+      # The Solaris linker doesn't like our version script for the libjpeg API
+      # library, but the version script for the TurboJPEG API library should
+      # still work.
+      file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map
+        "VERS_1 { global: foo;  local: *; }; VERS_2 { global: foo2; } VERS_1;")
+      set(CMAKE_REQUIRED_FLAGS "-Wl,-M,${CMAKE_CURRENT_BINARY_DIR}/conftest.map -shared")
+      check_c_source_compiles("int foo() { return 0; } int foo2() { return 2; }"
+        HAVE_MAPFILE)
+      set(CMAKE_REQUIRED_FLAGS)
+      file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map)
+      if(HAVE_MAPFILE)
+        message(STATUS "Linker supports mapfiles")
+        set(TJMAPFLAG "-Wl,-M,")
+      else()
+        message(STATUS "Linker does not support mapfiles")
+      endif()
+    endif()
+  endif()
+endif()
+
+# Generate files
+if(WIN32)
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/win/jconfig.h.in jconfig.h)
+else()
+  configure_file(jconfig.h.in jconfig.h)
+endif()
+configure_file(jconfigint.h.in jconfigint.h)
+configure_file(jversion.h.in jversion.h)
+if(UNIX)
+  configure_file(libjpeg.map.in libjpeg.map)
+endif()
+
+# Include directories and compiler definitions
+include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR})
+
+
+###############################################################################
+# TARGETS
+###############################################################################
+
+if(CMAKE_EXECUTABLE_SUFFIX_TMP)
+  set(CMAKE_EXECUTABLE_SUFFIX ${CMAKE_EXECUTABLE_SUFFIX_TMP})
+endif()
+message(STATUS "CMAKE_EXECUTABLE_SUFFIX = ${CMAKE_EXECUTABLE_SUFFIX}")
+
+set(JPEG_SOURCES jcapimin.c jcapistd.c jccoefct.c jccolor.c jcdctmgr.c jchuff.c
+  jcicc.c jcinit.c jcmainct.c jcmarker.c jcmaster.c jcomapi.c jcparam.c
+  jcphuff.c jcprepct.c jcsample.c jctrans.c jdapimin.c jdapistd.c jdatadst.c
+  jdatasrc.c jdcoefct.c jdcolor.c jddctmgr.c jdhuff.c jdicc.c jdinput.c
+  jdmainct.c jdmarker.c jdmaster.c jdmerge.c jdphuff.c jdpostct.c jdsample.c
+  jdtrans.c jerror.c jfdctflt.c jfdctfst.c jfdctint.c jidctflt.c jidctfst.c
+  jidctint.c jidctred.c jquant1.c jquant2.c jutils.c jmemmgr.c jmemnobs.c)
+
+if(WITH_ARITH_ENC OR WITH_ARITH_DEC)
+  set(JPEG_SOURCES ${JPEG_SOURCES} jaricom.c)
+endif()
+
+if(WITH_ARITH_ENC)
+  set(JPEG_SOURCES ${JPEG_SOURCES} jcarith.c)
+endif()
+
+if(WITH_ARITH_DEC)
+  set(JPEG_SOURCES ${JPEG_SOURCES} jdarith.c)
+endif()
+
+if(WITH_SIMD)
+  add_subdirectory(simd)
+  if(NEON_INTRINSICS)
+    add_definitions(-DNEON_INTRINSICS)
+  endif()
+elseif(NOT WITH_12BIT)
+  message(STATUS "SIMD extensions: None (WITH_SIMD = ${WITH_SIMD})")
+endif()
+if(WITH_SIMD)
+  message(STATUS "SIMD extensions: ${CPU_TYPE} (WITH_SIMD = ${WITH_SIMD})")
+  if(MSVC_IDE OR XCODE)
+    set_source_files_properties(${SIMD_OBJS} PROPERTIES GENERATED 1)
+  endif()
+else()
+  add_library(simd OBJECT jsimd_none.c)
+  if(NOT WIN32 AND (CMAKE_POSITION_INDEPENDENT_CODE OR ENABLE_SHARED))
+    set_target_properties(simd PROPERTIES POSITION_INDEPENDENT_CODE 1)
+  endif()
+endif()
+
+if(WITH_JAVA)
+  add_subdirectory(java)
+endif()
+
+if(ENABLE_SHARED)
+  add_subdirectory(sharedlib)
+endif()
+
+if(ENABLE_STATIC)
+  add_library(jpeg-static STATIC ${JPEG_SOURCES} $<TARGET_OBJECTS:simd>
+    ${SIMD_OBJS})
+  if(NOT MSVC)
+    set_target_properties(jpeg-static PROPERTIES OUTPUT_NAME jpeg)
+  endif()
+endif()
+
+if(WITH_TURBOJPEG)
+  if(ENABLE_SHARED)
+    set(TURBOJPEG_SOURCES ${JPEG_SOURCES} $<TARGET_OBJECTS:simd> ${SIMD_OBJS}
+      turbojpeg.c transupp.c jdatadst-tj.c jdatasrc-tj.c rdbmp.c rdppm.c
+      wrbmp.c wrppm.c)
+    set(TJMAPFILE ${CMAKE_CURRENT_SOURCE_DIR}/turbojpeg-mapfile)
+    if(WITH_JAVA)
+      set(TURBOJPEG_SOURCES ${TURBOJPEG_SOURCES} turbojpeg-jni.c)
+      include_directories(${JAVA_INCLUDE_PATH} ${JAVA_INCLUDE_PATH2})
+      set(TJMAPFILE ${CMAKE_CURRENT_SOURCE_DIR}/turbojpeg-mapfile.jni)
+    endif()
+    if(MSVC)
+      configure_file(${CMAKE_SOURCE_DIR}/win/turbojpeg.rc.in
+        ${CMAKE_BINARY_DIR}/win/turbojpeg.rc)
+      set(TURBOJPEG_SOURCES ${TURBOJPEG_SOURCES}
+        ${CMAKE_BINARY_DIR}/win/turbojpeg.rc)
+    endif()
+    add_library(turbojpeg SHARED ${TURBOJPEG_SOURCES})
+    set_property(TARGET turbojpeg PROPERTY COMPILE_FLAGS
+      "-DBMP_SUPPORTED -DPPM_SUPPORTED")
+    if(WIN32)
+      set_target_properties(turbojpeg PROPERTIES DEFINE_SYMBOL DLLDEFINE)
+    endif()
+    if(MINGW)
+      set_target_properties(turbojpeg PROPERTIES LINK_FLAGS -Wl,--kill-at)
+    endif()
+    if(APPLE AND (NOT CMAKE_OSX_DEPLOYMENT_TARGET OR
+                  CMAKE_OSX_DEPLOYMENT_TARGET VERSION_GREATER 10.4))
+      if(NOT CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG)
+        set(CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG "-Wl,-rpath,")
+      endif()
+      set_target_properties(turbojpeg PROPERTIES MACOSX_RPATH 1)
+    endif()
+    set_target_properties(turbojpeg PROPERTIES
+      SOVERSION ${TURBOJPEG_SO_MAJOR_VERSION} VERSION ${TURBOJPEG_SO_VERSION})
+    if(TJMAPFLAG)
+      set_target_properties(turbojpeg PROPERTIES
+        LINK_FLAGS "${TJMAPFLAG}${TJMAPFILE}")
+    endif()
+  endif()
+
+  if(ENABLE_STATIC)
+    add_library(turbojpeg-static STATIC ${JPEG_SOURCES} $<TARGET_OBJECTS:simd>
+      ${SIMD_OBJS} turbojpeg.c transupp.c jdatadst-tj.c jdatasrc-tj.c rdbmp.c
+      rdppm.c wrbmp.c wrppm.c)
+    set_property(TARGET turbojpeg-static PROPERTY COMPILE_FLAGS
+      "-DBMP_SUPPORTED -DPPM_SUPPORTED")
+    if(NOT MSVC)
+      set_target_properties(turbojpeg-static PROPERTIES OUTPUT_NAME turbojpeg)
+    endif()
+  endif()
+endif()
+
+if(WIN32)
+  set(USE_SETMODE "-DUSE_SETMODE")
+endif()
+if(WITH_12BIT)
+  set(COMPILE_FLAGS "-DGIF_SUPPORTED -DPPM_SUPPORTED ${USE_SETMODE}")
+else()
+  set(COMPILE_FLAGS "-DBMP_SUPPORTED -DGIF_SUPPORTED -DPPM_SUPPORTED -DTARGA_SUPPORTED ${USE_SETMODE}")
+  set(CJPEG_BMP_SOURCES rdbmp.c rdtarga.c)
+  set(DJPEG_BMP_SOURCES wrbmp.c wrtarga.c)
+endif()

cmake/CMakeLists.png

@@ -0,0 +1,741 @@
+# CMakeLists.txt
+
+# Copyright (C) 2018 Cosmin Truta
+# Copyright (C) 2007,2009-2018 Glenn Randers-Pehrson
+# Written by Christian Ehrlicher, 2007
+# Revised by Roger Lowman, 2009-2010
+# Revised by Clifford Yapp, 2011-2012,2017
+# Revised by Roger Leigh, 2016
+# Revised by Andreas Franek, 2016
+# Revised by Sam Serrels, 2017
+# Revised by Vadim Barkov, 2017
+# Revised by Vicky Pfau, 2018
+# Revised by Cameron Cawley, 2018
+# Revised by Cosmin Truta, 2018
+# Revised by Kyle Bentley, 2018
+
+# This code is released under the libpng license.
+# For conditions of distribution and use, see the disclaimer
+# and license in png.h
+
+cmake_minimum_required(VERSION 3.10)
+cmake_policy(VERSION 3.1)
+# When using CMake 3.4 and later, don't export symbols from executables unless
+# the CMAKE_ENABLE_EXPORTS variable is set.
+if(POLICY CMP0065)
+  cmake_policy(SET CMP0065 NEW)
+endif()
+if (POLICY CMP0077)
+  cmake_policy(SET CMP0077 NEW)
+endif()
+set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
+
+project(libpng C ASM)
+enable_testing()
+
+set(PNGLIB_MAJOR 1)
+set(PNGLIB_MINOR 6)
+set(PNGLIB_RELEASE 37)
+set(PNGLIB_NAME libpng${PNGLIB_MAJOR}${PNGLIB_MINOR})
+set(PNGLIB_VERSION ${PNGLIB_MAJOR}.${PNGLIB_MINOR}.${PNGLIB_RELEASE})
+
+include(GNUInstallDirs)
+
+# needed packages
+
+# Allow users to specify location of Zlib.
+# Useful if zlib is being built alongside this as a sub-project.
+option(PNG_BUILD_ZLIB "Custom zlib Location, else find_package is used" ON)
+
+if(NOT PNG_BUILD_ZLIB)
+  find_package(ZLIB REQUIRED)
+  include_directories(${ZLIB_INCLUDE_DIR})
+endif()
+
+if(UNIX AND NOT APPLE AND NOT BEOS AND NOT HAIKU)
+  find_library(M_LIBRARY m)
+else()
+  # libm is not needed and/or not available
+  set(M_LIBRARY "")
+endif()
+
+# COMMAND LINE OPTIONS
+option(PNG_SHARED "Build shared lib" OFF)
+option(PNG_STATIC "Build static lib" ON)
+option(PNG_TESTS  "Build libpng tests" OFF)
+
+# Many more configuration options could be added here
+option(PNG_FRAMEWORK "Build OS X framework" OFF)
+option(PNG_DEBUG "Build with debug output" OFF)
+option(PNG_HARDWARE_OPTIMIZATIONS "Enable hardware optimizations" OFF)
+
+set(PNG_PREFIX "" CACHE STRING "Prefix to add to the API function names")
+set(DFA_XTRA "" CACHE FILEPATH "File containing extra configuration settings")
+
+if(PNG_HARDWARE_OPTIMIZATIONS)
+
+# set definitions and sources for arm
+if(CMAKE_SYSTEM_PROCESSOR MATCHES "^arm" OR
+  CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64")
+  set(PNG_ARM_NEON_POSSIBLE_VALUES check on off)
+  set(PNG_ARM_NEON "check" CACHE STRING "Enable ARM NEON optimizations:
+     check: (default) use internal checking code;
+     off: disable the optimizations;
+     on: turn on unconditionally.")
+  set_property(CACHE PNG_ARM_NEON PROPERTY STRINGS
+     ${PNG_ARM_NEON_POSSIBLE_VALUES})
+  list(FIND PNG_ARM_NEON_POSSIBLE_VALUES ${PNG_ARM_NEON} index)
+  if(index EQUAL -1)
+    message(FATAL_ERROR
+            "PNG_ARM_NEON must be one of [${PNG_ARM_NEON_POSSIBLE_VALUES}]")
+  elseif(NOT ${PNG_ARM_NEON} STREQUAL "off")
+    set(libpng_arm_sources
+      arm/arm_init.c
+      arm/filter_neon.S
+      arm/filter_neon_intrinsics.c
+      arm/palette_neon_intrinsics.c)
+
+    if(${PNG_ARM_NEON} STREQUAL "on")
+      add_definitions(-DPNG_ARM_NEON_OPT=2)
+    elseif(${PNG_ARM_NEON} STREQUAL "check")
+      add_definitions(-DPNG_ARM_NEON_CHECK_SUPPORTED)
+    endif()
+  else()
+    add_definitions(-DPNG_ARM_NEON_OPT=0)
+  endif()
+endif()
+
+# set definitions and sources for powerpc
+if(CMAKE_SYSTEM_PROCESSOR MATCHES "^powerpc*" OR
+   CMAKE_SYSTEM_PROCESSOR MATCHES "^ppc64*")
+  set(PNG_POWERPC_VSX_POSSIBLE_VALUES on off)
+  set(PNG_POWERPC_VSX "on" CACHE STRING "Enable POWERPC VSX optimizations:
+     off: disable the optimizations.")
+  set_property(CACHE PNG_POWERPC_VSX PROPERTY STRINGS
+     ${PNG_POWERPC_VSX_POSSIBLE_VALUES})
+  list(FIND PNG_POWERPC_VSX_POSSIBLE_VALUES ${PNG_POWERPC_VSX} index)
+  if(index EQUAL -1)
+    message(FATAL_ERROR
+            "PNG_POWERPC_VSX must be one of [${PNG_POWERPC_VSX_POSSIBLE_VALUES}]")
+  elseif(NOT ${PNG_POWERPC_VSX} STREQUAL "off")
+    set(libpng_powerpc_sources
+      powerpc/powerpc_init.c
+      powerpc/filter_vsx_intrinsics.c)
+    if(${PNG_POWERPC_VSX} STREQUAL "on")
+      add_definitions(-DPNG_POWERPC_VSX_OPT=2)
+    endif()
+  else()
+    add_definitions(-DPNG_POWERPC_VSX_OPT=0)
+  endif()
+endif()
+
+# set definitions and sources for intel
+if(CMAKE_SYSTEM_PROCESSOR MATCHES "^i?86" OR
+   CMAKE_SYSTEM_PROCESSOR MATCHES "^x86_64*")
+  set(PNG_INTEL_SSE_POSSIBLE_VALUES on off)
+  set(PNG_INTEL_SSE "on" CACHE STRING "Enable INTEL_SSE optimizations:
+     off: disable the optimizations")
+  set_property(CACHE PNG_INTEL_SSE PROPERTY STRINGS
+     ${PNG_INTEL_SSE_POSSIBLE_VALUES})
+  list(FIND PNG_INTEL_SSE_POSSIBLE_VALUES ${PNG_INTEL_SSE} index)
+  if(index EQUAL -1)
+    message(FATAL_ERROR
+            "PNG_INTEL_SSE must be one of [${PNG_INTEL_SSE_POSSIBLE_VALUES}]")
+  elseif(NOT ${PNG_INTEL_SSE} STREQUAL "off")
+    set(libpng_intel_sources
+      intel/intel_init.c
+      intel/filter_sse2_intrinsics.c)
+    if(${PNG_INTEL_SSE} STREQUAL "on")
+      add_definitions(-DPNG_INTEL_SSE_OPT=1)
+    endif()
+  else()
+    add_definitions(-DPNG_INTEL_SSE_OPT=0)
+  endif()
+endif()
+
+# set definitions and sources for MIPS
+if(CMAKE_SYSTEM_PROCESSOR MATCHES "mipsel*" OR
+   CMAKE_SYSTEM_PROCESSOR MATCHES "mips64el*")
+  set(PNG_MIPS_MSA_POSSIBLE_VALUES on off)
+  set(PNG_MIPS_MSA "on" CACHE STRING "Enable MIPS_MSA optimizations:
+     off: disable the optimizations")
+  set_property(CACHE PNG_MIPS_MSA PROPERTY STRINGS
+     ${PNG_MIPS_MSA_POSSIBLE_VALUES})
+  list(FIND PNG_MIPS_MSA_POSSIBLE_VALUES ${PNG_MIPS_MSA} index)
+  if(index EQUAL -1)
+    message(FATAL_ERROR
+            "PNG_MIPS_MSA must be one of [${PNG_MIPS_MSA_POSSIBLE_VALUES}]")
+  elseif(NOT ${PNG_MIPS_MSA} STREQUAL "off")
+    set(libpng_mips_sources
+      mips/mips_init.c
+      mips/filter_msa_intrinsics.c)
+    if(${PNG_MIPS_MSA} STREQUAL "on")
+      add_definitions(-DPNG_MIPS_MSA_OPT=2)
+    endif()
+  else()
+    add_definitions(-DPNG_MIPS_MSA_OPT=0)
+  endif()
+endif()
+
+else(PNG_HARDWARE_OPTIMIZATIONS)
+
+# set definitions and sources for arm
+if(CMAKE_SYSTEM_PROCESSOR MATCHES "^arm" OR
+   CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64")
+  add_definitions(-DPNG_ARM_NEON_OPT=0)
+endif()
+
+# set definitions and sources for powerpc
+if(CMAKE_SYSTEM_PROCESSOR MATCHES "^powerpc*" OR
+   CMAKE_SYSTEM_PROCESSOR MATCHES "^ppc64*")
+  add_definitions(-DPNG_POWERPC_VSX_OPT=0)
+endif()
+
+# set definitions and sources for intel
+if(CMAKE_SYSTEM_PROCESSOR MATCHES "^i?86" OR
+   CMAKE_SYSTEM_PROCESSOR MATCHES "^x86_64*")
+  add_definitions(-DPNG_INTEL_SSE_OPT=0)
+endif()
+
+# set definitions and sources for MIPS
+if(CMAKE_SYSTEM_PROCESSOR MATCHES "mipsel*" OR
+   CMAKE_SYSTEM_PROCESSOR MATCHES "mips64el*")
+  add_definitions(-DPNG_MIPS_MSA_OPT=0)
+endif()
+
+endif(PNG_HARDWARE_OPTIMIZATIONS)
+
+# SET LIBNAME
+set(PNG_LIB_NAME png${PNGLIB_MAJOR}${PNGLIB_MINOR})
+
+# to distinguish between debug and release lib
+set(CMAKE_DEBUG_POSTFIX "d")
+
+include(CheckCSourceCompiles)
+option(ld-version-script "Enable linker version script" ON)
+if(ld-version-script AND NOT APPLE)
+  # Check if LD supports linker scripts.
+  file(WRITE "${CMAKE_CURRENT_BINARY_DIR}/conftest.map" "VERS_1 {
+        global: sym;
+        local: *;
+};
+
+VERS_2 {
+        global: sym2;
+                main;
+} VERS_1;
+")
+  set(CMAKE_REQUIRED_FLAGS_SAVE ${CMAKE_REQUIRED_FLAGS})
+  set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS} "-Wl,--version-script='${CMAKE_CURRENT_BINARY_DIR}/conftest.map'")
+  check_c_source_compiles("void sym(void) {}
+void sym2(void) {}
+int main(void) {return 0;}
+" HAVE_LD_VERSION_SCRIPT)
+  if(NOT HAVE_LD_VERSION_SCRIPT)
+    set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS_SAVE} "-Wl,-M -Wl,${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
+  check_c_source_compiles("void sym(void) {}
+void sym2(void) {}
+int main(void) {return 0;}
+" HAVE_SOLARIS_LD_VERSION_SCRIPT)
+  endif()
+  set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS_SAVE})
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
+endif()
+
+# Find symbol prefix.  Likely obsolete and unnecessary with recent
+# toolchains (it's not done in many other projects).
+function(symbol_prefix)
+  set(SYMBOL_PREFIX)
+
+  execute_process(COMMAND "${CMAKE_C_COMPILER}" "-E" "-"
+                  INPUT_FILE /dev/null
+                  OUTPUT_VARIABLE OUT
+                  RESULT_VARIABLE STATUS)
+
+  if(CPP_FAIL)
+    message(WARNING "Failed to run the C preprocessor")
+  endif()
+
+  string(REPLACE "\n" ";" OUT "${OUT}")
+  foreach(line ${OUT})
+    string(REGEX MATCH "^PREFIX=" found_match "${line}")
+    if(found_match)
+      string(REGEX REPLACE "^PREFIX=(.*\)" "\\1" prefix "${line}")
+      string(REGEX MATCH "__USER_LABEL_PREFIX__" found_match "${prefix}")
+      if(found_match)
+        string(REGEX REPLACE "(.*)__USER_LABEL_PREFIX__(.*)" "\\1\\2" prefix "${prefix}")
+      endif()
+      set(SYMBOL_PREFIX "${prefix}")
+    endif()
+  endforeach()
+
+  message(STATUS "Symbol prefix: ${SYMBOL_PREFIX}")
+  set(SYMBOL_PREFIX "${SYMBOL_PREFIX}" PARENT_SCOPE)
+endfunction()
+
+if(UNIX)
+  symbol_prefix()
+endif()
+
+find_program(AWK NAMES gawk awk)
+
+include_directories(${CMAKE_CURRENT_BINARY_DIR})
+
+if(NOT AWK OR ANDROID)
+  # No awk available to generate sources; use pre-built pnglibconf.h
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.h.prebuilt
+                 ${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h)
+  add_custom_target(genfiles) # Dummy
+else()
+  include(CMakeParseArguments)
+  # Generate .chk from .out with awk
+  # generate_chk(INPUT inputfile OUTPUT outputfile [DEPENDS dep1 [dep2...]])
+  function(generate_chk)
+    set(options)
+    set(oneValueArgs INPUT OUTPUT)
+    set(multiValueArgs DEPENDS)
+    cmake_parse_arguments(_GC "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+    if(NOT _GC_INPUT)
+      message(FATAL_ERROR "generate_chk: Missing INPUT argument")
+    endif()
+    if(NOT _GC_OUTPUT)
+      message(FATAL_ERROR "generate_chk: Missing OUTPUT argument")
+    endif()
+
+    add_custom_command(OUTPUT "${_GC_OUTPUT}"
+                       COMMAND "${CMAKE_COMMAND}"
+                               "-DINPUT=${_GC_INPUT}"
+                               "-DOUTPUT=${_GC_OUTPUT}"
+                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/genchk.cmake"
+                       DEPENDS "${_GC_INPUT}" ${_GC_DEPENDS}
+                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
+  endfunction()
+
+  # Generate .out from .c with awk
+  # generate_out(INPUT inputfile OUTPUT outputfile [DEPENDS dep1 [dep2...]])
+  function(generate_out)
+    set(options)
+    set(oneValueArgs INPUT OUTPUT)
+    set(multiValueArgs DEPENDS)
+    cmake_parse_arguments(_GO "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+    if(NOT _GO_INPUT)
+      message(FATAL_ERROR "generate_out: Missing INPUT argument")
+    endif()
+    if(NOT _GO_OUTPUT)
+      message(FATAL_ERROR "generate_out: Missing OUTPUT argument")
+    endif()
+
+    add_custom_command(OUTPUT "${_GO_OUTPUT}"
+                       COMMAND "${CMAKE_COMMAND}"
+                               "-DINPUT=${_GO_INPUT}"
+                               "-DOUTPUT=${_GO_OUTPUT}"
+                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/genout.cmake"
+                       DEPENDS "${_GO_INPUT}" ${_GO_DEPENDS}
+                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
+  endfunction()
+
+  # Generate specific source file with awk
+  # generate_source(OUTPUT outputfile [DEPENDS dep1 [dep2...]])
+  function(generate_source)
+    set(options)
+    set(oneValueArgs OUTPUT)
+    set(multiValueArgs DEPENDS)
+    cmake_parse_arguments(_GSO "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+    if(NOT _GSO_OUTPUT)
+      message(FATAL_ERROR "generate_source: Missing OUTPUT argument")
+    endif()
+
+    add_custom_command(OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/${_GSO_OUTPUT}"
+                       COMMAND "${CMAKE_COMMAND}"
+                               "-DOUTPUT=${_GSO_OUTPUT}"
+                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake"
+                       DEPENDS ${_GSO_DEPENDS}
+                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
+  endfunction()
+
+  # Copy file
+  function(generate_copy source destination)
+    add_custom_command(OUTPUT "${destination}"
+                       COMMAND "${CMAKE_COMMAND}" -E remove "${destination}"
+                       COMMAND "${CMAKE_COMMAND}" -E copy "${source}"
+                                                          "${destination}"
+                       DEPENDS "${source}")
+  endfunction()
+
+  # Generate scripts/pnglibconf.h
+  generate_source(OUTPUT "scripts/pnglibconf.c"
+                  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.dfa"
+                          "${CMAKE_CURRENT_SOURCE_DIR}/scripts/options.awk"
+                          "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h")
+
+  # Generate pnglibconf.c
+  generate_source(OUTPUT "pnglibconf.c"
+                  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.dfa"
+                          "${CMAKE_CURRENT_SOURCE_DIR}/scripts/options.awk"
+                          "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h")
+
+  if(PNG_PREFIX)
+    set(PNGLIBCONF_H_EXTRA_DEPENDS
+        "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
+        "${CMAKE_CURRENT_SOURCE_DIR}/scripts/macro.lst")
+    set(PNGPREFIX_H_EXTRA_DEPENDS
+        "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out")
+  endif()
+
+  generate_out(INPUT "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.c"
+               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out")
+
+  # Generate pnglibconf.h
+  generate_source(OUTPUT "pnglibconf.h"
+                  DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out"
+                          ${PNGLIBCONF_H_EXTRA_DEPENDS})
+
+  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/intprefix.c"
+               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out"
+               DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
+
+  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/prefix.c"
+               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
+               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
+                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
+                       "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out")
+
+  # Generate pngprefix.h
+  generate_source(OUTPUT "pngprefix.h"
+                  DEPENDS ${PNGPREFIX_H_EXTRA_DEPENDS})
+
+  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/sym.c"
+               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
+               DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
+
+  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/symbols.c"
+               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
+               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
+                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
+                       "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.h.prebuilt")
+
+  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/vers.c"
+               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out"
+               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
+                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
+                       "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
+
+  generate_chk(INPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
+               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk"
+               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/checksym.awk"
+                       "${CMAKE_CURRENT_SOURCE_DIR}/scripts/symbols.def")
+
+  add_custom_target(symbol-check DEPENDS
+                    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk")
+
+  generate_copy("${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
+                "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym")
+  generate_copy("${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out"
+                "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers")
+
+  add_custom_target(genvers DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers")
+  add_custom_target(gensym DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym")
+
+  add_custom_target("genprebuilt"
+                    COMMAND "${CMAKE_COMMAND}"
+                            "-DOUTPUT=scripts/pnglibconf.h.prebuilt"
+                            -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake"
+                    WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
+
+  # A single target handles generation of all generated files.  If
+  # they are depended upon separately by multiple targets, this
+  # confuses parallel make (it would require a separate top-level
+  # target for each file to track the dependencies properly).
+  add_custom_target(genfiles DEPENDS
+    "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym"
+    "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers"
+    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.c"
+    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h"
+    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out"
+    "${CMAKE_CURRENT_BINARY_DIR}/pngprefix.h"
+    "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out"
+    "${CMAKE_CURRENT_BINARY_DIR}/scripts/pnglibconf.c"
+    "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
+    "${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
+    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk"
+    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
+    "${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out")
+endif(NOT AWK OR ANDROID)
+
+# OUR SOURCES
+set(libpng_public_hdrs
+  png.h
+  pngconf.h
+  "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h"
+)
+set(libpng_private_hdrs
+  pngpriv.h
+  pngdebug.h
+  pnginfo.h
+  pngstruct.h
+)
+if(AWK AND NOT ANDROID)
+  list(APPEND libpng_private_hdrs "${CMAKE_CURRENT_BINARY_DIR}/pngprefix.h")
+endif()
+set(libpng_sources
+  ${libpng_public_hdrs}
+  ${libpng_private_hdrs}
+  png.c
+  pngerror.c
+  pngget.c
+  pngmem.c
+  pngpread.c
+  pngread.c
+  pngrio.c
+  pngrtran.c
+  pngrutil.c
+  pngset.c
+  pngtrans.c
+  pngwio.c
+  pngwrite.c
+  pngwtran.c
+  pngwutil.c
+  ${libpng_arm_sources}
+  ${libpng_intel_sources}
+  ${libpng_mips_sources}
+  ${libpng_powerpc_sources}
+)
+set(pngtest_sources
+  pngtest.c
+)
+set(pngvalid_sources
+  contrib/libtests/pngvalid.c
+)
+set(pngstest_sources
+  contrib/libtests/pngstest.c
+)
+set(pngunknown_sources
+  contrib/libtests/pngunknown.c
+)
+set(pngimage_sources
+  contrib/libtests/pngimage.c
+)
+set(pngfix_sources
+  contrib/tools/pngfix.c
+)
+set(png_fix_itxt_sources
+  contrib/tools/png-fix-itxt.c
+)
+
+if(MSVC)
+  add_definitions(-D_CRT_SECURE_NO_DEPRECATE)
+endif()
+
+if(PNG_DEBUG)
+  add_definitions(-DPNG_DEBUG)
+endif()
+
+# NOW BUILD OUR TARGET
+include_directories(${CMAKE_CURRENT_SOURCE_DIR} ${ZLIB_INCLUDE_DIR})
+
+unset(PNG_LIB_TARGETS)
+
+if(PNG_STATIC)
+  # does not work without changing name
+  set(PNG_LIB_NAME_STATIC png_static)
+  add_library(png_static STATIC ${libpng_sources})
+  add_dependencies(png_static genfiles)
+  # MSVC doesn't use a different file extension for shared vs. static
+  # libs.  We are able to change OUTPUT_NAME to remove the _static
+  # for all other platforms.
+  if(NOT MSVC)
+    set_target_properties(png_static PROPERTIES
+      OUTPUT_NAME "${PNG_LIB_NAME}"
+      CLEAN_DIRECT_OUTPUT 1)
+  else()
+    set_target_properties(png_static PROPERTIES
+      OUTPUT_NAME "${PNG_LIB_NAME}_static"
+      CLEAN_DIRECT_OUTPUT 1)
+  endif()
+  list(APPEND PNG_LIB_TARGETS png_static)
+  if(MSVC)
+    # msvc does not append 'lib' - do it here to have consistent name
+    set_target_properties(png_static PROPERTIES PREFIX "lib")
+  endif()
+  target_link_libraries(png_static ${M_LIBRARY})
+endif()
+
+if(NOT PNG_LIB_TARGETS)
+  message(SEND_ERROR
+    "No library variant selected to build. "
+    "Please enable at least one of the following options: "
+    "PNG_STATIC, PNG_SHARED, PNG_FRAMEWORK")
+endif()
+
+# Set a variable with CMake code which:
+# Creates a symlink from src to dest (if possible) or alternatively
+# copies if different.
+include(CMakeParseArguments)
+
+function(create_symlink DEST_FILE)
+
+  cmake_parse_arguments(S "" "FILE;TARGET" "" ${ARGN})
+
+  if(NOT S_TARGET AND NOT S_FILE)
+    message(FATAL_ERROR "create_symlink: Missing TARGET or FILE argument")
+  endif()
+
+  if(S_TARGET AND S_FILE)
+    message(FATAL_ERROR "create_symlink: Both source file ${S_FILE} and build target ${S_TARGET} arguments are present; can only have one.")
+  endif()
+
+  if(S_FILE)
+    # If we don't need to symlink something that's coming from a build target,
+    # we can go ahead and symlink/copy at configure time.
+    if(CMAKE_HOST_WIN32 AND NOT CYGWIN)
+      execute_process(
+        COMMAND "${CMAKE_COMMAND}" -E copy_if_different ${S_FILE} ${DEST_FILE}
+        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
+    else()
+      execute_process(
+        COMMAND ${CMAKE_COMMAND} -E create_symlink ${S_FILE} ${DEST_FILE}
+        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
+    endif()
+  endif()
+
+  if(S_TARGET)
+    # We need to use generator expressions, which can be a bit tricky, so for
+    # simplicity make the symlink a POST_BUILD step and use the TARGET
+    # signature of add_custom_command.
+    if(CMAKE_HOST_WIN32 AND NOT CYGWIN)
+      add_custom_command(TARGET ${S_TARGET} POST_BUILD
+        COMMAND "${CMAKE_COMMAND}" -E copy_if_different $<TARGET_LINKER_FILE_NAME:${S_TARGET}> $<TARGET_LINKER_FILE_DIR:${S_TARGET}>/${DEST_FILE})
+    else()
+      add_custom_command(TARGET ${S_TARGET} POST_BUILD
+        COMMAND "${CMAKE_COMMAND}" -E create_symlink $<TARGET_LINKER_FILE_NAME:${S_TARGET}> $<TARGET_LINKER_FILE_DIR:${S_TARGET}>/${DEST_FILE})
+    endif()
+  endif()
+
+endfunction()
+
+# Create source generation scripts.
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/genchk.cmake.in
+               ${CMAKE_CURRENT_BINARY_DIR}/scripts/genchk.cmake @ONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/genout.cmake.in
+               ${CMAKE_CURRENT_BINARY_DIR}/scripts/genout.cmake @ONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/gensrc.cmake.in
+               ${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake @ONLY)
+
+# libpng is a library so default to 'lib'
+if(NOT DEFINED CMAKE_INSTALL_LIBDIR)
+  set(CMAKE_INSTALL_LIBDIR lib)
+endif()
+
+# CREATE PKGCONFIG FILES
+# We use the same files like ./configure, so we have to set its vars.
+# Only do this on Windows for Cygwin - the files don't make much sense outside
+# of a UNIX look-alike.
+if(NOT WIN32 OR CYGWIN OR MINGW)
+  set(prefix      ${CMAKE_INSTALL_PREFIX})
+  set(exec_prefix ${CMAKE_INSTALL_PREFIX})
+  set(libdir      ${CMAKE_INSTALL_FULL_LIBDIR})
+  set(includedir  ${CMAKE_INSTALL_FULL_INCLUDEDIR})
+  set(LIBS        "-lz -lm")
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libpng.pc.in
+    ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc @ONLY)
+  create_symlink(libpng.pc FILE ${PNGLIB_NAME}.pc)
+
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libpng-config.in
+    ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config @ONLY)
+  create_symlink(libpng-config FILE ${PNGLIB_NAME}-config)
+endif()
+
+# SET UP LINKS
+if(PNG_SHARED)
+  set_target_properties(png PROPERTIES
+#   VERSION 16.${PNGLIB_RELEASE}.1.6.37
+    VERSION 16.${PNGLIB_RELEASE}.0
+    SOVERSION 16
+    CLEAN_DIRECT_OUTPUT 1)
+endif()
+
+# INSTALL
+if(NOT SKIP_INSTALL_LIBRARIES AND NOT SKIP_INSTALL_ALL)
+  install(TARGETS ${PNG_LIB_TARGETS}
+          EXPORT libpng
+          RUNTIME DESTINATION bin
+          LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+          ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+          FRAMEWORK DESTINATION ${CMAKE_INSTALL_LIBDIR})
+
+  if(PNG_SHARED)
+    # Create a symlink for libpng.dll.a => libpng16.dll.a on Cygwin
+    if(CYGWIN OR MINGW)
+      create_symlink(libpng${CMAKE_IMPORT_LIBRARY_SUFFIX} TARGET png)
+      install(FILES $<TARGET_LINKER_FILE_DIR:png>/libpng${CMAKE_IMPORT_LIBRARY_SUFFIX}
+              DESTINATION ${CMAKE_INSTALL_LIBDIR})
+    endif()
+
+    if(NOT WIN32)
+      create_symlink(libpng${CMAKE_SHARED_LIBRARY_SUFFIX} TARGET png)
+      install(FILES $<TARGET_LINKER_FILE_DIR:png>/libpng${CMAKE_SHARED_LIBRARY_SUFFIX}
+              DESTINATION ${CMAKE_INSTALL_LIBDIR})
+    endif()
+  endif()
+
+  if(PNG_STATIC)
+    if(NOT WIN32 OR CYGWIN OR MINGW)
+      create_symlink(libpng${CMAKE_STATIC_LIBRARY_SUFFIX} TARGET png_static)
+      install(FILES $<TARGET_LINKER_FILE_DIR:png_static>/libpng${CMAKE_STATIC_LIBRARY_SUFFIX}
+              DESTINATION ${CMAKE_INSTALL_LIBDIR})
+    endif()
+  endif()
+endif()
+
+if(NOT SKIP_INSTALL_HEADERS AND NOT SKIP_INSTALL_ALL)
+  install(FILES ${libpng_public_hdrs} DESTINATION include)
+  install(FILES ${libpng_public_hdrs} DESTINATION include/${PNGLIB_NAME})
+endif()
+if(NOT SKIP_INSTALL_EXECUTABLES AND NOT SKIP_INSTALL_ALL)
+  if(NOT WIN32 OR CYGWIN OR MINGW)
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/libpng-config DESTINATION bin)
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config DESTINATION bin)
+  endif()
+endif()
+
+if(NOT SKIP_INSTALL_PROGRAMS AND NOT SKIP_INSTALL_ALL)
+  install(TARGETS ${PNG_BIN_TARGETS}
+          RUNTIME DESTINATION bin)
+endif()
+
+if(NOT SKIP_INSTALL_FILES AND NOT SKIP_INSTALL_ALL)
+  # Install man pages
+  if(NOT PNG_MAN_DIR)
+    set(PNG_MAN_DIR "share/man")
+  endif()
+  install(FILES libpng.3 libpngpf.3 DESTINATION ${PNG_MAN_DIR}/man3)
+  install(FILES png.5 DESTINATION ${PNG_MAN_DIR}/man5)
+  # Install pkg-config files
+  if(NOT CMAKE_HOST_WIN32 OR CYGWIN OR MINGW)
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libpng.pc
+            DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/libpng-config
+            DESTINATION bin)
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc
+            DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config
+            DESTINATION bin)
+  endif()
+endif()
+
+# Create an export file that CMake users can include() to import our targets.
+if(NOT SKIP_INSTALL_EXPORT AND NOT SKIP_INSTALL_ALL)
+  install(EXPORT libpng DESTINATION lib/libpng FILE lib${PNG_LIB_NAME}.cmake)
+endif()
+
+# what's with libpng-manual.txt and all the extra files?
+
+# UNINSTALL
+# do we need this?
+
+# DIST
+# do we need this?
+
+# to create msvc import lib for mingw compiled shared lib
+# pexports libpng.dll > libpng.def
+# lib /def:libpng.def /machine:x86

cmake/CMakeLists.txt

@@ -107,7 +107,7 @@ endif()
 
 # silence excessive warnings for new Intel Compilers
 if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
-  set(CMAKE_TUNE_DEFAULT "-Wno-tautological-constant-compare")
+  set(CMAKE_TUNE_DEFAULT "-Wno-tautological-constant-compare -Wno-unused-command-line-argument")
 endif()
 
 # silence excessive warnings for PGI/NVHPC compilers
@@ -116,7 +116,7 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
 endif()
 
 # silence nvcc warnings
-if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA))
+if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
   set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
 endif()
 
@@ -135,9 +135,14 @@ set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
 # ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
 # and prints lots of pointless warnings about "unsafe" functions
 if(MSVC)
-  add_compile_options(/Zc:__cplusplus)
-  add_compile_options(/wd4244)
-  add_compile_options(/wd4267)
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
+    add_compile_options(/Zc:__cplusplus)
+    add_compile_options(/wd4244)
+    add_compile_options(/wd4267)
+    if(LAMMPS_EXCEPTIONS)
+      add_compile_options(/EHsc)
+    endif()
+  endif()
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
@@ -161,10 +166,12 @@ option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared lib
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
 option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
 
-# allow enabling clang-tidy for C++ files
+# Support using clang-tidy for C++ files with selected options
 set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
 if(ENABLE_CLANG_TIDY)
-  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=*-header-filter=.*" CACHE STRING "")
+  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
+else()
+  unset(CMAKE_CXX_CLANG_TIDY CACHE)
 endif()
 
 include(GNUInstallDirs)
@@ -328,7 +335,9 @@ string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
 target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES})
 
 # posix_memalign is not available on Windows
-if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+# with INTEL package and Intel compilers we use TBB's aligned malloc
+if((CMAKE_SYSTEM_NAME STREQUAL "Windows")
+   AND NOT (PKG_INTEL AND ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))))
   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")
@@ -777,14 +786,16 @@ if(BUILD_SHARED_LIBS)
     find_package(Python COMPONENTS Interpreter)
   endif()
   if(BUILD_IS_MULTI_CONFIG)
-    set(LIBLAMMPS_SHARED_BINARY ${CMAKE_BINARY_DIR}/$<CONFIG>/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
+    set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>)
   else()
-    set(LIBLAMMPS_SHARED_BINARY ${CMAKE_BINARY_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
+    set(MY_BUILD_DIR ${CMAKE_BINARY_DIR})
   endif()
+  set(LIBLAMMPS_SHARED_BINARY ${MY_BUILD_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
   if(Python_EXECUTABLE)
     add_custom_target(
       install-python ${CMAKE_COMMAND} -E remove_directory build
-      COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps -l ${LIBLAMMPS_SHARED_BINARY}
+      COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
+              -l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR}
       COMMENT "Installing LAMMPS Python module")
   else()
     add_custom_target(
@@ -947,6 +958,12 @@ if(PKG_KSPACE)
       else()
         message(STATUS "Kokkos FFT: cuFFT")
       endif()
+    elseif(Kokkos_ENABLE_HIP)
+      if(FFT STREQUAL "KISS")
+        message(STATUS "Kokkos FFT: KISS")
+      else()
+        message(STATUS "Kokkos FFT: hipFFT")
+      endif()
     else()
       message(STATUS "Kokkos FFT: ${FFT}")
     endif()

cmake/CMakeLists.zlib

@@ -0,0 +1,195 @@
+cmake_minimum_required(VERSION 3.10)
+# When using CMake 3.4 and later, don't export symbols from executables unless
+# the CMAKE_ENABLE_EXPORTS variable is set.
+if(POLICY CMP0065)
+  cmake_policy(SET CMP0065 NEW)
+endif()
+if (POLICY CMP0077)
+  cmake_policy(SET CMP0077 NEW)
+endif()
+set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
+
+project(zlib C)
+
+set(VERSION "1.2.11")
+
+option(ASM686 "Enable building i686 assembly implementation" OFF)
+option(AMD64 "Enable building amd64 assembly implementation" OFF)
+
+set(INSTALL_BIN_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for executables")
+set(INSTALL_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib" CACHE PATH "Installation directory for libraries")
+set(INSTALL_INC_DIR "${CMAKE_INSTALL_PREFIX}/include" CACHE PATH "Installation directory for headers")
+set(INSTALL_MAN_DIR "${CMAKE_INSTALL_PREFIX}/share/man" CACHE PATH "Installation directory for manual pages")
+set(INSTALL_PKGCONFIG_DIR "${CMAKE_INSTALL_PREFIX}/share/pkgconfig" CACHE PATH "Installation directory for pkgconfig (.pc) files")
+
+include(CheckTypeSize)
+include(CheckFunctionExists)
+include(CheckIncludeFile)
+include(CheckCSourceCompiles)
+
+check_include_file(sys/types.h HAVE_SYS_TYPES_H)
+check_include_file(stdint.h    HAVE_STDINT_H)
+check_include_file(stddef.h    HAVE_STDDEF_H)
+
+#
+# Check to see if we have large file support
+#
+set(CMAKE_REQUIRED_DEFINITIONS -D_LARGEFILE64_SOURCE=1)
+# We add these other definitions here because CheckTypeSize.cmake
+# in CMake 2.4.x does not automatically do so and we want
+# compatibility with CMake 2.4.x.
+if(HAVE_SYS_TYPES_H)
+    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_SYS_TYPES_H)
+endif()
+if(HAVE_STDINT_H)
+    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDINT_H)
+endif()
+if(HAVE_STDDEF_H)
+    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDDEF_H)
+endif()
+check_type_size(off64_t OFF64_T)
+check_type_size(off64_t OFF64_T)
+if(HAVE_OFF64_T)
+   add_definitions(-D_LARGEFILE64_SOURCE=1)
+endif()
+set(CMAKE_REQUIRED_DEFINITIONS) # clear variable
+
+#
+# Check for fseeko
+#
+check_function_exists(fseeko HAVE_FSEEKO)
+if(NOT HAVE_FSEEKO)
+    add_definitions(-DNO_FSEEKO)
+endif()
+
+#
+# Check for unistd.h
+#
+check_include_file(unistd.h Z_HAVE_UNISTD_H)
+
+if(MSVC)
+    set(CMAKE_DEBUG_POSTFIX "d")
+    add_definitions(-D_CRT_SECURE_NO_DEPRECATE)
+    add_definitions(-D_CRT_NONSTDC_NO_DEPRECATE)
+    include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+endif()
+
+if(NOT CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
+    # If we're doing an out of source build and the user has a zconf.h
+    # in their source tree...
+    if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h)
+        file(RENAME ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.included)
+  endif()
+endif()
+
+set(ZLIB_PC ${CMAKE_CURRENT_BINARY_DIR}/zlib.pc)
+configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/zlib.pc.cmakein
+		${ZLIB_PC} @ONLY)
+configure_file(	${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.cmakein
+		${CMAKE_CURRENT_BINARY_DIR}/zconf.h @ONLY)
+include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_SOURCE_DIR})
+
+
+#============================================================================
+# zlib
+#============================================================================
+
+set(ZLIB_PUBLIC_HDRS
+    ${CMAKE_CURRENT_BINARY_DIR}/zconf.h
+    zlib.h
+)
+set(ZLIB_PRIVATE_HDRS
+    crc32.h
+    deflate.h
+    gzguts.h
+    inffast.h
+    inffixed.h
+    inflate.h
+    inftrees.h
+    trees.h
+    zutil.h
+)
+set(ZLIB_SRCS
+    adler32.c
+    compress.c
+    crc32.c
+    deflate.c
+    gzclose.c
+    gzlib.c
+    gzread.c
+    gzwrite.c
+    inflate.c
+    infback.c
+    inftrees.c
+    inffast.c
+    trees.c
+    uncompr.c
+    zutil.c
+)
+
+if(NOT MINGW)
+    set(ZLIB_DLL_SRCS
+        win32/zlib1.rc # If present will override custom build rule below.
+    )
+endif()
+
+if(CMAKE_COMPILER_IS_GNUCC)
+    if(ASM686)
+        set(ZLIB_ASMS contrib/asm686/match.S)
+    elseif (AMD64)
+        set(ZLIB_ASMS contrib/amd64/amd64-match.S)
+    endif ()
+
+	if(ZLIB_ASMS)
+		add_definitions(-DASMV)
+		set_source_files_properties(${ZLIB_ASMS} PROPERTIES LANGUAGE C COMPILE_FLAGS -DNO_UNDERLINE)
+	endif()
+endif()
+
+if(MSVC)
+    if(ASM686)
+		ENABLE_LANGUAGE(ASM_MASM)
+        set(ZLIB_ASMS
+			contrib/masmx86/inffas32.asm
+			contrib/masmx86/match686.asm
+		)
+    elseif (AMD64)
+		ENABLE_LANGUAGE(ASM_MASM)
+        set(ZLIB_ASMS
+			contrib/masmx64/gvmat64.asm
+			contrib/masmx64/inffasx64.asm
+		)
+    endif()
+
+	if(ZLIB_ASMS)
+		add_definitions(-DASMV -DASMINF)
+	endif()
+endif()
+
+# parse the full version number from zlib.h and include in ZLIB_FULL_VERSION
+file(READ ${CMAKE_CURRENT_SOURCE_DIR}/zlib.h _zlib_h_contents)
+string(REGEX REPLACE ".*#define[ \t]+ZLIB_VERSION[ \t]+\"([-0-9A-Za-z.]+)\".*"
+    "\\1" ZLIB_FULL_VERSION ${_zlib_h_contents})
+
+if(MINGW)
+    # This gets us DLL resource information when compiling on MinGW.
+    if(NOT CMAKE_RC_COMPILER)
+        set(CMAKE_RC_COMPILER windres.exe)
+    endif()
+
+    add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
+                       COMMAND ${CMAKE_RC_COMPILER}
+                            -D GCC_WINDRES
+                            -I ${CMAKE_CURRENT_SOURCE_DIR}
+                            -I ${CMAKE_CURRENT_BINARY_DIR}
+                            -o ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
+                            -i ${CMAKE_CURRENT_SOURCE_DIR}/win32/zlib1.rc)
+    set(ZLIB_DLL_SRCS ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj)
+endif(MINGW)
+
+add_library(zlibstatic STATIC ${ZLIB_SRCS} ${ZLIB_ASMS} ${ZLIB_PUBLIC_HDRS} ${ZLIB_PRIVATE_HDRS})
+
+if(UNIX)
+    # On unix-like platforms the library is almost always called libz
+   set_target_properties(zlibstatic PROPERTIES OUTPUT_NAME z)
+endif()

cmake/CMakeSettings.json

@@ -8,7 +8,7 @@
       "installRoot": "${workspaceRoot}\\install\\${name}",
       "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
       "buildCommandArgs": "",
-      "ctestCommandArgs": "",
+      "ctestCommandArgs": "-V",
       "inheritEnvironments": [ "msvc_x64_x64" ],
       "variables": [
         {
@@ -26,11 +26,6 @@
           "value": "True",
           "type": "BOOL"
         },
-        {
-          "name": "PKG_PYTHON",
-          "value": "True",
-          "type": "BOOL"
-        },
         {
           "name": "ENABLE_TESTING",
           "value": "True",
@@ -46,7 +41,7 @@
       "installRoot": "${workspaceRoot}\\install\\${name}",
       "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
       "buildCommandArgs": "",
-      "ctestCommandArgs": "",
+      "ctestCommandArgs": "-V",
       "inheritEnvironments": [ "msvc_x64_x64" ],
       "variables": [
         {
@@ -64,11 +59,6 @@
           "value": "True",
           "type": "BOOL"
         },
-        {
-          "name": "PKG_PYTHON",
-          "value": "True",
-          "type": "BOOL"
-        },
         {
           "name": "ENABLE_TESTING",
           "value": "True",
@@ -102,11 +92,6 @@
           "value": "True",
           "type": "BOOL"
         },
-        {
-          "name": "PKG_PYTHON",
-          "value": "True",
-          "type": "BOOL"
-        },
         {
           "name": "ENABLE_TESTING",
           "value": "True",
@@ -122,7 +107,7 @@
       "installRoot": "${workspaceRoot}\\install\\${name}",
       "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
       "buildCommandArgs": "",
-      "ctestCommandArgs": "",
+      "ctestCommandArgs": "-V",
       "inheritEnvironments": [ "clang_cl_x64" ],
       "variables": [
         {
@@ -141,7 +126,40 @@
           "type": "BOOL"
         },
         {
-          "name": "PKG_PYTHON",
+          "name": "ENABLE_TESTING",
+          "value": "True",
+          "type": "BOOL"
+        }
+      ]
+    },
+    {
+      "name": "x64-Debug-IntelLLVM",
+      "generator": "Ninja",
+      "configurationType": "Debug",
+      "buildRoot": "${workspaceRoot}\\build\\${name}",
+      "installRoot": "${workspaceRoot}\\install\\${name}",
+      "buildCommandArgs": "",
+      "ctestCommandArgs": "-V",
+      "inheritEnvironments": [],
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-llvm.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
+      "variables": [
+        {
+          "name": "PKG_ELECTRODE",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_SHARED_LIBS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_TOOLS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "LAMMPS_EXCEPTIONS",
           "value": "True",
           "type": "BOOL"
         },
@@ -149,8 +167,142 @@
           "name": "ENABLE_TESTING",
           "value": "True",
           "type": "BOOL"
+        },
+        {
+          "name": "FFT",
+          "value": "MKL",
+          "type": "STRING"
+        }
+      ]
+    },
+    {
+      "name": "x64-Release-IntelLLVM",
+      "generator": "Ninja",
+      "configurationType": "Release",
+      "buildRoot": "${workspaceRoot}\\build\\${name}",
+      "installRoot": "${workspaceRoot}\\install\\${name}",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-llvm.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
+      "buildCommandArgs": "",
+      "ctestCommandArgs": "-V",
+      "inheritEnvironments": [],
+      "variables": [
+        {
+          "name": "PKG_ELECTRODE",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_SHARED_LIBS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_TOOLS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "LAMMPS_EXCEPTIONS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "ENABLE_TESTING",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "FFT",
+          "value": "MKL",
+          "type": "STRING"
+        }
+      ]
+    },
+    {
+      "name": "x64-Debug-Intel-Classic",
+      "generator": "Ninja",
+      "configurationType": "Debug",
+      "buildRoot": "${workspaceRoot}\\build\\${name}",
+      "installRoot": "${workspaceRoot}\\install\\${name}",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-classic.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
+      "buildCommandArgs": "",
+      "ctestCommandArgs": "-V",
+      "inheritEnvironments": [],
+      "variables": [
+        {
+          "name": "PKG_ELECTRODE",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_SHARED_LIBS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_TOOLS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "LAMMPS_EXCEPTIONS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "ENABLE_TESTING",
+          "value": "False",
+          "type": "BOOL"
+        },
+        {
+          "name": "FFT",
+          "value": "MKL",
+          "type": "STRING"
+        }
+      ]
+    },
+    {
+      "name": "x64-Release-Intel-Classic",
+      "generator": "Ninja",
+      "configurationType": "Release",
+      "buildRoot": "${workspaceRoot}\\build\\${name}",
+      "installRoot": "${workspaceRoot}\\install\\${name}",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-classic.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
+      "buildCommandArgs": "",
+      "ctestCommandArgs": "-V",
+      "inheritEnvironments": [],
+      "variables": [
+        {
+          "name": "PKG_ELECTRODE",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_SHARED_LIBS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_TOOLS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "LAMMPS_EXCEPTIONS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "ENABLE_TESTING",
+          "value": "False",
+          "type": "BOOL"
+        },
+        {
+          "name": "FFT",
+          "value": "MKL",
+          "type": "STRING"
         }
       ]
     }
   ]
-}
+}

cmake/Modules/LAMMPSInterfacePlugin.cmake

@@ -0,0 +1,197 @@
+# CMake script code to define LAMMPS settings required for building LAMMPS plugins
+
+# enforce out-of-source build
+if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
+  message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
+    "Please remove CMakeCache.txt and CMakeFiles first.")
+endif()
+
+# global LAMMPS/plugin build settings
+set(LAMMPS_SOURCE_DIR ""  CACHE PATH "Location of LAMMPS sources folder")
+if(NOT LAMMPS_SOURCE_DIR)
+  message(FATAL_ERROR "Must set LAMMPS_SOURCE_DIR")
+endif()
+
+# by default, install into $HOME/.local (not /usr/local),
+# so that no root access (and sudo) is needed
+if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
+endif()
+
+# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
+# and prints lots of pointless warnings about "unsafe" functions
+if(MSVC)
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
+    add_compile_options(/Zc:__cplusplus)
+    add_compile_options(/wd4244)
+    add_compile_options(/wd4267)
+    if(LAMMPS_EXCEPTIONS)
+      add_compile_options(/EHsc)
+    endif()
+  endif()
+  add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
+endif()
+
+# C++11 is required
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+# Need -restrict with Intel compilers
+if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+endif()
+set(CMAKE_POSITION_INDEPENDENT_CODE TRUE)
+
+#######
+# helper functions from LAMMPSUtils.cmake
+function(validate_option name values)
+  string(TOLOWER ${${name}} needle_lower)
+  string(TOUPPER ${${name}} needle_upper)
+  list(FIND ${values} ${needle_lower} IDX_LOWER)
+  list(FIND ${values} ${needle_upper} IDX_UPPER)
+  if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
+    list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
+    message(FATAL_ERROR "\n########################################################################\n"
+      "Invalid value '${${name}}' for option ${name}\n"
+      "\n"
+      "Possible values are:\n"
+      "${POSSIBLE_VALUE_LIST}"
+      "########################################################################")
+  endif()
+endfunction(validate_option)
+
+# helper function for getting the most recently modified file or folder from a glob pattern
+function(get_newest_file path variable)
+  file(GLOB _dirs ${path})
+  set(_besttime 2000-01-01T00:00:00)
+  set(_bestfile "<unknown>")
+  foreach(_dir ${_dirs})
+    file(TIMESTAMP ${_dir} _newtime)
+    if(_newtime IS_NEWER_THAN _besttime)
+      set(_bestfile ${_dir})
+      set(_besttime ${_newtime})
+    endif()
+  endforeach()
+  if(_bestfile STREQUAL "<unknown>")
+    message(FATAL_ERROR "Could not find valid path at: ${path}")
+  endif()
+  set(${variable} ${_bestfile} PARENT_SCOPE)
+endfunction()
+
+#################################################################################
+# LAMMPS C++ interface. We only need the header related parts except on windows.
+add_library(lammps INTERFACE)
+target_include_directories(lammps INTERFACE ${LAMMPS_SOURCE_DIR})
+if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
+  target_link_libraries(lammps INTERFACE ${CMAKE_BINARY_DIR}/../liblammps.dll.a)
+endif()
+
+################################################################################
+# MPI configuration
+if(NOT CMAKE_CROSSCOMPILING)
+  find_package(MPI QUIET)
+  option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
+else()
+  option(BUILD_MPI "Build MPI version" OFF)
+endif()
+
+if(BUILD_MPI)
+  # do not include the (obsolete) MPI C++ bindings which makes
+  # for leaner object files and avoids namespace conflicts
+  set(MPI_CXX_SKIP_MPICXX TRUE)
+  # We use a non-standard procedure to cross-compile with MPI on Windows
+  if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
+    # Download and configure custom MPICH files for Windows
+    message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
+    set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
+    set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
+    set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
+    set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
+    mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+    mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
+    mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+    mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
+
+    include(ExternalProject)
+    if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+      ExternalProject_Add(mpi4win_build
+        URL     ${MPICH2_WIN64_DEVEL_URL}
+        URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+        CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+        BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+    else()
+      ExternalProject_Add(mpi4win_build
+        URL     ${MPICH2_WIN32_DEVEL_URL}
+        URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
+        CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+        BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+    endif()
+
+    ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+    file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+    add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+    set_target_properties(MPI::MPI_CXX PROPERTIES
+      IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
+      INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+      INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+    add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+    # set variables for status reporting at the end of CMake run
+    set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+    set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+    set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
+  else()
+    find_package(MPI REQUIRED)
+    option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
+    if(LAMMPS_LONGLONG_TO_LONG)
+      target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)
+    endif()
+  endif()
+  target_link_libraries(lammps INTERFACE MPI::MPI_CXX)
+else()
+  add_library(mpi_stubs INTERFACE)
+  target_include_directories(mpi_stubs INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
+  target_link_libraries(lammps INTERFACE mpi_stubs)
+endif()
+
+################################################################################
+# detect if we may enable OpenMP support by default
+set(BUILD_OMP_DEFAULT OFF)
+find_package(OpenMP QUIET)
+if(OpenMP_FOUND)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  if(HAVE_OMP_H_INCLUDE)
+    set(BUILD_OMP_DEFAULT ON)
+  endif()
+endif()
+
+option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
+
+if(BUILD_OMP)
+  find_package(OpenMP REQUIRED)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  if(NOT HAVE_OMP_H_INCLUDE)
+    message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
+  endif()
+
+  if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
+      (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
+    # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
+    # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
+    target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4)
+  else()
+    target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3)
+  endif()
+  target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX)
+endif()
+
+################
+# integer size selection
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
+set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
+set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
+validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
+string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
+target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES})

cmake/Modules/LAMMPSUtils.cmake

@@ -24,6 +24,24 @@ function(validate_option name values)
     endif()
 endfunction(validate_option)
 
+# helper function for getting the most recently modified file or folder from a glob pattern
+function(get_newest_file path variable)
+  file(GLOB _dirs ${path})
+  set(_besttime 2000-01-01T00:00:00)
+  set(_bestfile "<unknown>")
+  foreach(_dir ${_dirs})
+    file(TIMESTAMP ${_dir} _newtime)
+    if(_newtime IS_NEWER_THAN _besttime)
+      set(_bestfile ${_dir})
+      set(_besttime ${_newtime})
+    endif()
+  endforeach()
+  if(_bestfile STREQUAL "<unknown>")
+    message(FATAL_ERROR "Could not find valid path at: ${path}")
+  endif()
+  set(${variable} ${_bestfile} PARENT_SCOPE)
+endfunction()
+
 function(get_lammps_version version_header variable)
     file(STRINGS ${version_header} line REGEX LAMMPS_VERSION)
     set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)

cmake/Modules/Packages/INTEL.cmake

@@ -38,7 +38,7 @@ if(INTEL_LRT_MODE STREQUAL "C++11")
   endif()
 endif()
 
-if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
   if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
     message(FATAL_ERROR "INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
   endif()
@@ -46,12 +46,12 @@ else()
   message(WARNING "INTEL gives best performance with Intel compilers")
 endif()
 
-find_package(TBB_MALLOC QUIET)
+find_package(TBB_MALLOC)
 if(TBB_MALLOC_FOUND)
   target_link_libraries(lammps PRIVATE TBB::TBB_MALLOC)
 else()
   target_compile_definitions(lammps PRIVATE -DLMP_INTEL_NO_TBB)
-  if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+  if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
     message(WARNING "INTEL with Intel compilers should use TBB malloc libraries")
   endif()
 endif()

cmake/Modules/Packages/KOKKOS.cmake

@@ -47,8 +47,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.5.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "079323d973ae0e1c38c0a54a150c674e" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.6.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "b5c44ea961031795f434002cd7b31c20" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   ExternalProject_Add(kokkos_build
@@ -72,7 +72,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.5.00 REQUIRED CONFIG)
+  find_package(Kokkos 3.6.00 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
   target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()
@@ -130,6 +130,11 @@ if(PKG_KSPACE)
       target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
       target_link_libraries(lammps PRIVATE cufft)
     endif()
+  elseif(Kokkos_ENABLE_HIP)
+    if(NOT (FFT STREQUAL "KISS"))
+      target_compile_definitions(lammps PRIVATE -DFFT_HIPFFT)
+      target_link_libraries(lammps PRIVATE hipfft)
+    endif()
   endif()
 endif()
 

cmake/Modules/Packages/MDI.cmake

@@ -50,6 +50,7 @@ if(DOWNLOAD_MDI)
     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
     -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
     -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+    -DCMAKE_POSITION_INDEPENDENT_CODE=ON
     -Dlanguage=C
     -Dlibtype=STATIC
     -Dmpi=${MDI_USE_MPI}

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,6 +1,6 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "a2ac3315c41a1a4a5c912bcb1bc9c5cc" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_MD5 "32394d799bc282bb57696c78c456e64f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 
@@ -13,8 +13,12 @@ execute_process(
   COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
   WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
 )
+get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
 
-file(GLOB lib-pace ${CMAKE_BINARY_DIR}/lammps-user-pace-*)
+# enforce building libyaml-cpp as static library and turn off optional features
+set(YAML_BUILD_SHARED_LIBS OFF)
+set(YAML_CPP_BUILD_CONTRIB OFF)
+set(YAML_CPP_BUILD_TOOLS OFF)
 add_subdirectory(${lib-pace}/yaml-cpp build-yaml-cpp)
 set(YAML_CPP_INCLUDE_DIR ${lib-pace}/yaml-cpp/include)
 
@@ -28,5 +32,6 @@ target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_
 
 
 target_link_libraries(pace PRIVATE yaml-cpp-pace)
-
-target_link_libraries(lammps PRIVATE pace)
+if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+  target_link_libraries(lammps PRIVATE pace)
+endif()

cmake/Modules/Packages/ML-QUIP.cmake

@@ -43,6 +43,7 @@ if(DOWNLOAD_QUIP)
   file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}")
 
   message(STATUS "QUIP download via git requested - we will build our own")
+  set(CMAKE_EP_GIT_REMOTE_UPDATE_STRATEGY CHECKOUT)
   # QUIP has no releases (except for a tag marking the end of Python 2 support). We use the current "public" branch
   # The LAMMPS interface wrapper has a compatibility constant that is being checked at runtime.
   include(ExternalProject)

cmake/Modules/Tools.cmake

@@ -3,6 +3,9 @@ if(BUILD_TOOLS)
   target_compile_definitions(binary2txt PRIVATE -DLAMMPS_${LAMMPS_SIZES})
   install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
 
+  add_executable(stl_bin2txt ${LAMMPS_TOOLS_DIR}/stl_bin2txt.cpp)
+  install(TARGETS stl_bin2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
+
   include(CheckGeneratorSupport)
   if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
     include(CheckLanguage)

cmake/Modules/generate_lmpgitversion.cmake

@@ -31,5 +31,7 @@ set(temp "${temp}const char *LAMMPS_NS::LAMMPS::git_descriptor() { return \"${te
 set(temp "${temp}#endif\n\n")
 
 message(STATUS "Generating lmpgitversion.h...")
-file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" )
-execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")
+
+string(REPLACE "\\ " " " LAMMPS_GIT_HEADER "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")
+file(WRITE "${LAMMPS_GIT_HEADER}.tmp" "${temp}" )
+execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_GIT_HEADER}.tmp" "${LAMMPS_GIT_HEADER}")

cmake/presets/kokkos-cuda.cmake

@@ -3,7 +3,9 @@
 # that is compatible with all higher CC, but not the default CC 3.5
 set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
-set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)
 set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
+
+# hide deprecation warnings temporarily for stable release
+set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

cmake/presets/kokkos-hip.cmake

@@ -0,0 +1,20 @@
+# preset that enables KOKKOS and selects HIP compilation with OpenMP
+# enabled as well. Also sets some performance related compiler flags.
+set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_CUDA   OFF CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_HIP    ON CACHE BOOL "" FORCE)
+set(Kokkos_ARCH_VEGA90A on CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS ON CACHE BOOL "" FORCE)
+set(BUILD_OMP ON CACHE BOOL "" FORCE)
+
+set(CMAKE_CXX_COMPILER hipcc CACHE STRING "" FORCE)
+set(CMAKE_TUNE_FLAGS "-munsafe-fp-atomics" CACHE STRING "" FORCE)
+
+# hide deprecation warnings temporarily for stable release
+set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
+
+# these flags are needed to build with Cray MPICH on OLCF Crusher
+#-D CMAKE_CXX_FLAGS="-I/${MPICH_DIR}/include"
+#-D MPI_CXX_LIBRARIES="-L${MPICH_DIR}/lib -lmpi -L${CRAY_MPICH_ROOTDIR}/gtl/lib -lmpi_gtl_hsa"

cmake/presets/kokkos-openmp.cmake

@@ -4,3 +4,6 @@ set(Kokkos_ENABLE_SERIAL ON  CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_OPENMP ON  CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   OFF CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
+
+# hide deprecation warnings temporarily for stable release
+set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

cmake/presets/kokkos-serial.cmake

@@ -3,3 +3,6 @@ set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_SERIAL ON  CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_OPENMP OFF CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   OFF CACHE BOOL "" FORCE)
+
+# hide deprecation warnings temporarily for stable release
+set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

cmake/presets/kokkos-sycl.cmake

@@ -8,6 +8,9 @@ set(Kokkos_ENABLE_SYCL   ON CACHE BOOL "" FORCE)
 set(Kokkos_ARCH_MAXWELL50 on CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
 
+# hide deprecation warnings temporarily for stable release
+set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
+
 set(CMAKE_CXX_COMPILER clang++ CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -46,8 +46,8 @@ set(WIN_PACKAGES
   MISC
   ML-HDNNP
   ML-IAP
-  ML-SNAP
   ML-RANN
+  ML-SNAP
   MOFFF
   MOLECULE
   MOLFILE
@@ -56,6 +56,7 @@ set(WIN_PACKAGES
   ORIENT
   PERI
   PHONON
+  PLUGIN
   POEMS
   PTM
   QEQ

cmake/presets/windows-intel-classic.cmake

@@ -0,0 +1,8 @@
+# preset that will enable Intel compilers with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "icl" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "icl" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "ifort" CACHE STRING "" FORCE)
+
+unset(HAVE_OMP_H_INCLUDE CACHE)
+

cmake/presets/windows-intel-llvm.cmake

@@ -0,0 +1,8 @@
+# preset that will enable Intel compilers with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "icx" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
+set(INTEL_LRT_MODE "C++11" CACHE STRING "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+set(CMAKE_TUNE_FLAGS -Wno-unused-command-line-argument)

cmake/presets/windows.cmake

@@ -43,6 +43,7 @@ set(WIN_PACKAGES
   PERI
   PHONON
   POEMS
+  PLUGIN
   PTM
   QEQ
   QTB

doc/Makefile

@@ -13,6 +13,7 @@ VENV           = $(BUILDDIR)/docenv
 ANCHORCHECK    = $(VENV)/bin/rst_anchor_check
 SPHINXCONFIG   = $(BUILDDIR)/utils/sphinx-config
 MATHJAX        = $(SPHINXCONFIG)/_static/mathjax
+MATHJAXTAG     = 3.2.2
 
 PYTHON         = $(word 3,$(shell type python3))
 DOXYGEN        = $(word 3,$(shell type doxygen))
@@ -230,12 +231,13 @@ $(VENV):
 		$(PYTHON) -m venv $(VENV); \
 		. $(VENV)/bin/activate; \
 		pip $(PIP_OPTIONS) install --upgrade pip; \
+		pip $(PIP_OPTIONS) install --upgrade wheel; \
 		pip $(PIP_OPTIONS) install -r $(BUILDDIR)/utils/requirements.txt; \
 		deactivate;\
 	)
 
 $(MATHJAX):
-	@git clone -b 3.2.0 -c advice.detachedHead=0 --depth 1 https://github.com/mathjax/MathJax.git $@
+	@git clone -b $(MATHJAXTAG) -c advice.detachedHead=0 --depth 1 https://github.com/mathjax/MathJax.git $@
 
 $(ANCHORCHECK): $(VENV)
 	@( \

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "4 May 2022" "2022-5-4"
+.TH LAMMPS "1" "23 June 2022" "2022-6-23"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 24 March 2022
+\- Molecular Dynamics Simulator.  Version 23 June 2022
 
 .SH SYNOPSIS
 .B lmp

doc/src/Build_extras.rst

@@ -641,14 +641,27 @@ This list was last updated for version 3.5.0 of the Kokkos library.
 
          -D CMAKE_CXX_COMPILER=${HOME}/lammps/lib/kokkos/bin/nvcc_wrapper
 
-      To simplify compilation, four preset files are included in the
+      For AMD or NVIDIA GPUs using HIP, set these variables:
+
+      .. code-block:: bash
+
+         -D Kokkos_ARCH_HOSTARCH=yes   # HOSTARCH = HOST from list above
+         -D Kokkos_ARCH_GPUARCH=yes    # GPUARCH = GPU from list above
+         -D Kokkos_ENABLE_HIP=yes
+         -D Kokkos_ENABLE_OPENMP=yes
+
+      This will enable FFTs on the GPU, either by the internal KISSFFT library
+      or with the hipFFT wrapper library, which will call out to the
+      platform-appropriate vendor library: rocFFT on AMD GPUs or cuFFT on
+      NVIDIA GPUs.
+
+      To simplify compilation, five preset files are included in the
       ``cmake/presets`` folder, ``kokkos-serial.cmake``,
-      ``kokkos-openmp.cmake``, ``kokkos-cuda.cmake``, and
-      ``kokkos-sycl.cmake``.  They will enable the KOKKOS package and
-      enable some hardware choice.  So to compile with OpenMP host
-      parallelization, CUDA device parallelization (for GPUs with CC 5.0
-      and up) with some common packages enabled, you can do the
-      following:
+      ``kokkos-openmp.cmake``, ``kokkos-cuda.cmake``,
+      ``kokkos-hip.cmake``, and ``kokkos-sycl.cmake``.  They will enable
+      the KOKKOS package and enable some hardware choice.  So to compile
+      with CUDA device parallelization (for GPUs with CC 5.0 and up)
+      with some common packages enabled, you can do the following:
 
       .. code-block:: bash
 
@@ -707,6 +720,15 @@ This list was last updated for version 3.5.0 of the Kokkos library.
          KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
          CC = mpicxx -cxx=$(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
 
+      For AMD or NVIDIA GPUs using HIP:
+
+      .. code-block:: make
+
+         KOKKOS_DEVICES = HIP
+         KOKKOS_ARCH = HOSTARCH,GPUARCH  # HOSTARCH = HOST from list above that is hosting the GPU
+                                         # GPUARCH = GPU from list above
+         FFT_INC = -DFFT_HIPFFT           # enable use of hipFFT (optional)
+         FFT_LIB = -lhipfft               # link to hipFFT library
 
 Advanced KOKKOS compilation settings
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/src/Build_package.rst

@@ -150,7 +150,7 @@ other files dependent on that package are also excluded.
 .. _cmake_presets:
 
 CMake presets for installing many packages
-""""""""""""""""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Instead of specifying all the CMake options via the command-line,
 CMake allows initializing its settings cache using script files.
@@ -178,6 +178,11 @@ one of them as a starting point and customize it to your needs.
     cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake  # disable all packages
     mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross compilers
 
+Presets that have names starting with "windows" are specifically for
+compiling LAMMPS :doc:`natively on Windows <Build_windows>` and
+presets that have names starting with "kokkos" are specifically for
+selecting configurations for compiling LAMMPS with :ref:`KOKKOS <kokkos>`.
+
 .. note::
 
    Running cmake this way manipulates the CMake settings cache in your
@@ -220,7 +225,8 @@ These commands install/un-install sets of packages:
 .. code-block:: bash
 
     make yes-all                        # install all packages
-    make no-all                         # uninstall all packages
+    make no-all                         # check for changes and uninstall all packages
+    make no-installed                   # only check and uninstall installed packages
     make yes-basic                      # install a few commonly used packages'
     make no-basic                       # remove a few commonly used packages'
     make yes-most                       # install most packages w/o libs'

doc/src/Build_settings.rst

@@ -287,8 +287,8 @@ Output of JPG, PNG, and movie files
 
 The :doc:`dump image <dump_image>` command has options to output JPEG or
 PNG image files.  Likewise the :doc:`dump movie <dump_image>` command
-outputs movie files in MPEG format.  Using these options requires the
-following settings:
+outputs movie files in a variety of movie formats.  Using these options
+requires the following settings:
 
 .. tabs::
 
@@ -328,11 +328,12 @@ following settings:
          JPG_LIB = -ljpeg -lpng -lz       # library names
 
       As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
-      if make can find the graphics header and library files.  You must
-      specify ``JPG_LIB`` with a list of graphics libraries to include
-      in the link.  You must insure ffmpeg is in a directory where
-      LAMMPS can find it at runtime, that is a directory in your PATH
-      environment variable.
+      if make can find the graphics header and library files in their
+      default system locations.  You must specify ``JPG_LIB`` with a
+      list of graphics libraries to include in the link.  You must make
+      certain that the ffmpeg executable (or ffmpeg.exe on Windows) is
+      in a directory where LAMMPS can find it at runtime; that is
+      usually a directory list in your ``PATH`` environment variable.
 
 Using ``ffmpeg`` to output movie files requires that your machine
 supports the "popen" function in the standard runtime library.

doc/src/Build_windows.rst

@@ -5,6 +5,7 @@ Notes for building LAMMPS on Windows
 * :ref:`Running Linux on Windows <linux>`
 * :ref:`Using GNU GCC ported to Windows <gnu>`
 * :ref:`Using Visual Studio <msvc>`
+* :ref:`Using Intel oneAPI compilers and libraries <oneapi>`
 * :ref:`Using a cross-compiler <cross>`
 
 ----------
@@ -25,8 +26,10 @@ assistance in resolving portability issues.  This is particularly true
 for compiling LAMMPS on Windows, since this platform has significant
 differences in some low-level functionality.  As of LAMMPS version 14
 December 2021, large parts of LAMMPS can be compiled natively with the
-Microsoft Visual C++ Compilers.  This is largely facilitated by using
-the :doc:`Developer_platform` in the ``platform`` namespace.
+Microsoft Visual C++ Compilers.  As of LAMMPS version 31 May 2022, also
+the Intel oneAPI compilers can compile large parts of LAMMPS natively on
+Windows.  This is mostly facilitated by using the
+:doc:`Developer_platform` in the ``platform`` namespace and CMake.
 
 Before trying to build LAMMPS on Windows yourself, please consider the
 `pre-compiled Windows installer packages <https://packages.lammps.org/windows.html>`_
@@ -99,6 +102,10 @@ It is possible to use both the integrated CMake support of the Visual
 Studio IDE or use an external CMake installation (e.g. downloaded from
 cmake.org) to create build files and compile LAMMPS from the command line.
 
+Compilation via command line and unit tests are checked automatically
+for the LAMMPS development branch through
+`GitHub Actions <https://github.com/lammps/lammps/actions/workflows/compile-msvc.yml>`_.
+
 .. note::
 
    Versions of Visual Studio before version 17.1 may scan the entire
@@ -111,6 +118,10 @@ Please note, that for either approach CMake will create a so-called
 the command lines for building and testing LAMMPS must be adjusted
 accordingly.
 
+The LAMMPS cmake folder contains a ``CMakeSettings.json`` file with
+build configurations for MSVC compilers and the MS provided Clang
+compiler package in Debug and Release mode.
+
 To support running in parallel you can compile with OpenMP enabled using
 the OPENMP package or install Microsoft MPI (including the SDK) and compile
 LAMMPS with MPI enabled.
@@ -121,6 +132,53 @@ LAMMPS with MPI enabled.
    via GitHub or the `LAMMPS forum at MatSci <https://matsci.org/c/lammps/lammps-development/>`_,
    if you have questions or LAMMPS specific problems.
 
+.. _oneapi:
+
+Using Intel oneAPI Compilers and Libraries
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionadded:: 31May2022
+
+After installing the `Intel oneAPI
+<https://www.intel.com/content/www/us/en/developer/tools/oneapi/toolkits.html>`_
+base toolkit and the HPC toolkit, it is also possible to compile large
+parts of LAMMPS natively on Windows using Intel compilers.  The HPC
+toolkit provides two sets of C/C++ and Fortran compilers: the so-called
+"classic" compilers (``icl.exe`` and ``ifort.exe``) and newer, LLVM
+based compilers (``icx.exe`` and ``ifx.exe``).  In addition to the
+compilers and their dependent modules, also the thread building blocks
+(TBB) and the math kernel library (MKL) need to be installed.  Two
+presets (``cmake/presets/windows-intel-llvm.cmake`` and
+``cmake/presets/windows-intel-classic.cmake``) are provided for
+selecting the LLVM based or classic compilers, respectively. The preset
+``cmake/presets/windows.cmake`` enables compatible packages that are not
+dependent on additional features or libraries.  You **must** use the
+CMake based build procedure and use Ninja as build tool.  For compiling
+from the command prompt, thus both `CMake <https://cmake.org>`_ and
+`Ninja-build <https://ninja-build.org>`_ binaries must be installed.  It
+is also possible to use Visual Studio, if it is started (``devenv.exe``)
+from a command prompt that has the Intel oneAPI compilers enabled.  The
+Visual Studio settings file in the ``cmake`` folder contains
+configurations for both compiler variants in debug and release settings.
+Those will use the CMake and Ninja binaries bundled with Visual Studio,
+thus a separate installation is not required.
+
+.. admonition:: Known Limitations
+   :class: note
+
+   In addition to portability issues with several packages and external
+   libraries, the classic Intel compilers are currently not able to
+   compile the googletest libraries and thus enabling the ``-DENABLE_TESTING``
+   option will result in compilation failure.  The LLVM based compilers
+   are compatible.
+
+.. note::
+
+   This is work in progress and you should contact the LAMMPS developers
+   via GitHub or the `LAMMPS forum at MatSci <https://matsci.org/c/lammps/lammps-development/>`_,
+   if you have questions or LAMMPS specific problems.
+
+
 .. _cross:
 
 Using a cross-compiler
@@ -145,14 +203,3 @@ LAMMPS developers.  We instead rely on the feedback of the users
 of these pre-compiled LAMMPS packages for Windows.  We will try to resolve
 issues to the best of our abilities if we become aware of them. However
 this is subject to time constraints and focus on HPC platforms.
-
-.. _native:
-
-Native Visual C++ support
-^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Support for the Visual C++ compilers is currently not available. The
-CMake build system is capable of creating suitable a Visual Studio
-style build environment, but the LAMMPS source code itself is not
-ported to fully support Visual C++. Volunteers to take on this task
-are welcome.

doc/src/Commands_all.rst

@@ -14,7 +14,7 @@
 General commands
 ================
 
-An alphabetic list of all general LAMMPS commands.
+An alphabetic list of general LAMMPS commands.
 
 .. table_from_list::
    :columns: 5
@@ -47,35 +47,26 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`displace_atoms <displace_atoms>`
    * :doc:`dump <dump>`
    * :doc:`dump_modify <dump_modify>`
-   * :doc:`dynamical_matrix (k) <dynamical_matrix>`
    * :doc:`echo <echo>`
    * :doc:`fix <fix>`
    * :doc:`fix_modify <fix_modify>`
    * :doc:`group <group>`
-   * :doc:`group2ndx <group2ndx>`
-   * :doc:`hyper <hyper>`
    * :doc:`if <if>`
    * :doc:`improper_coeff <improper_coeff>`
    * :doc:`improper_style <improper_style>`
    * :doc:`include <include>`
    * :doc:`info <info>`
    * :doc:`jump <jump>`
-   * :doc:`kim <kim_commands>`
    * :doc:`kspace_modify <kspace_modify>`
    * :doc:`kspace_style <kspace_style>`
    * :doc:`label <label>`
    * :doc:`lattice <lattice>`
    * :doc:`log <log>`
    * :doc:`mass <mass>`
-   * :doc:`mdi <mdi>`
    * :doc:`minimize <minimize>`
    * :doc:`min_modify <min_modify>`
    * :doc:`min_style <min_style>`
-   * :doc:`min_style spin <min_spin>`
    * :doc:`molecule <molecule>`
-   * :doc:`ndx2group <group2ndx>`
-   * :doc:`neb <neb>`
-   * :doc:`neb/spin <neb_spin>`
    * :doc:`neigh_modify <neigh_modify>`
    * :doc:`neighbor <neighbor>`
    * :doc:`newton <newton>`
@@ -86,11 +77,8 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`pair_style <pair_style>`
    * :doc:`pair_write <pair_write>`
    * :doc:`partition <partition>`
-   * :doc:`plugin <plugin>`
-   * :doc:`prd <prd>`
    * :doc:`print <print>`
    * :doc:`processors <processors>`
-   * :doc:`python <python>`
    * :doc:`quit <quit>`
    * :doc:`read_data <read_data>`
    * :doc:`read_dump <read_dump>`
@@ -108,14 +96,9 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`shell <shell>`
    * :doc:`special_bonds <special_bonds>`
    * :doc:`suffix <suffix>`
-   * :doc:`tad <tad>`
-   * :doc:`temper <temper>`
-   * :doc:`temper/grem <temper_grem>`
-   * :doc:`temper/npt <temper_npt>`
    * :doc:`thermo <thermo>`
    * :doc:`thermo_modify <thermo_modify>`
    * :doc:`thermo_style <thermo_style>`
-   * :doc:`third_order (k) <third_order>`
    * :doc:`timer <timer>`
    * :doc:`timestep <timestep>`
    * :doc:`uncompute <uncompute>`
@@ -128,3 +111,27 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`write_data <write_data>`
    * :doc:`write_dump <write_dump>`
    * :doc:`write_restart <write_restart>`
+
+Additional general LAMMPS commands provided by packages.  A few
+commands have accelerated versions.  This is indicated by an
+additional letter in parenthesis: k = KOKKOS.
+
+.. table_from_list::
+   :columns: 5
+
+   * :doc:`dynamical_matrix (k) <dynamical_matrix>`
+   * :doc:`group2ndx <group2ndx>`
+   * :doc:`hyper <hyper>`
+   * :doc:`kim <kim_commands>`
+   * :doc:`mdi <mdi>`
+   * :doc:`ndx2group <group2ndx>`
+   * :doc:`neb <neb>`
+   * :doc:`neb/spin <neb_spin>`
+   * :doc:`plugin <plugin>`
+   * :doc:`prd <prd>`
+   * :doc:`python <python>`
+   * :doc:`tad <tad>`
+   * :doc:`temper <temper>`
+   * :doc:`temper/grem <temper_grem>`
+   * :doc:`temper/npt <temper_npt>`
+   * :doc:`third_order (k) <third_order>`

doc/src/Commands_bond.rst

@@ -88,7 +88,7 @@ OPT.
    * :doc:`dipole (o) <angle_dipole>`
    * :doc:`fourier (o) <angle_fourier>`
    * :doc:`fourier/simple (o) <angle_fourier_simple>`
-   * :doc:`gaussian <angle_gaussian>` - multicentered Gaussian-based angle potential
+   * :doc:`gaussian <angle_gaussian>`
    * :doc:`harmonic (iko) <angle_harmonic>`
    * :doc:`mm3 <angle_mm3>`
    * :doc:`quartic (o) <angle_quartic>`

doc/src/Commands_pair.rst

@@ -231,7 +231,7 @@ OPT.
    * :doc:`oxrna2/stk <pair_oxrna2>`
    * :doc:`oxrna2/xstk <pair_oxrna2>`
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
-   * :doc:`pace <pair_pace>`
+   * :doc:`pace (k) <pair_pace>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`
@@ -269,6 +269,7 @@ OPT.
    * :doc:`spin/neel <pair_spin_neel>`
    * :doc:`srp <pair_srp>`
    * :doc:`sw (giko) <pair_sw>`
+   * :doc:`sw/angle/table <pair_sw_angle_table>`
    * :doc:`sw/mod (o) <pair_sw>`
    * :doc:`table (gko) <pair_table>`
    * :doc:`table/rx (k) <pair_table_rx>`
@@ -279,6 +280,7 @@ OPT.
    * :doc:`tersoff/table (o) <pair_tersoff>`
    * :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>`
    * :doc:`thole <pair_thole>`
+   * :doc:`threebody/table <pair_threebody_table>`
    * :doc:`tip4p/cut (o) <pair_coul>`
    * :doc:`tip4p/long (o) <pair_coul>`
    * :doc:`tip4p/long/soft (o) <pair_fep_soft>`

doc/src/Commands_parse.rst

@@ -77,18 +77,19 @@ LAMMPS:
    so that you do not have to define (or discard) a temporary variable,
    "X" in this case.
 
-   Additionally, the "immediate" variable expression may be followed by
-   a colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
-   The format string must be appropriate for a double-precision
-   floating-point value.  The format string is used to output the result
-   of the variable expression evaluation.  If a format string is not
-   specified a high-precision "%.20g" is used as the default.
+   Additionally, the entire "immediate" variable expression may be
+   followed by a colon, followed by a C-style format string,
+   e.g. ":%f" or ":%.10g".  The format string must be appropriate for
+   a double-precision floating-point value.  The format string is used
+   to output the result of the variable expression evaluation.  If a
+   format string is not specified, a high-precision "%.20g" is used as
+   the default format.
 
    This can be useful for formatting print output to a desired precision:
 
    .. code-block:: LAMMPS
 
-      print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"
+      print "Final energy per atom: $(v_ke_per_atom+v_pe_per_atom:%10.3f) eV/atom"
 
    Note that neither the curly-bracket or immediate form of variables
    can contain nested $ characters for other variables to substitute

doc/src/Developer_plugins.rst

@@ -276,10 +276,27 @@ Compilation of the plugin can be managed via both, CMake or traditional
 GNU makefiles.  Some examples that can be used as a template are in the
 ``examples/plugins`` folder.  The CMake script code has some small
 adjustments to allow building the plugins for running unit tests with
-them. Another example that converts the KIM package into a plugin can be
-found in the ``examples/kim/plugin`` folder.  No changes to the sources
-of the KIM package themselves are needed; only the plugin interface and
-loader code needs to be added.  This example only supports building with
-CMake, but is probably a more typical example. To compile you need to
-run CMake with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>.  Other
+them.
+
+Another example that converts the KIM package into a plugin can be found
+in the ``examples/kim/plugin`` folder.  No changes to the sources of the
+KIM package themselves are needed; only the plugin interface and loader
+code needs to be added.  This example only supports building with CMake,
+but is probably a more typical example. To compile you need to run CMake
+with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>.  Other
 configuration setting are identical to those for compiling LAMMPS.
+
+A second example for a plugin from a package is in the
+``examples/PACKAGES/pace/plugin`` folder that will create a plugin from
+the ML-PACE package.  In this case the bulk of the code is in a static
+external library that is being downloaded and compiled first and then
+combined with the pair style wrapper and the plugin loader.  This
+example also contains a NSIS script that can be used to create an
+Installer package for Windows (the mutual licensing terms of the
+external library and LAMMPS conflict when distributing binaries, so the
+ML-PACE package cannot be linked statically, but the LAMMPS headers
+required to build the plugin are also available under a less restrictive
+license).  This will automatically set the required environment variable
+and launching a (compatible) LAMMPS binary will load and register the
+plugin and the ML-PACE package can then be used as it was linked into
+LAMMPS.

doc/src/Howto_body.rst

@@ -239,7 +239,7 @@ is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
 
 .. parsed-literal::
 
-   3 1 27
+   3 1 19
    4
    1 1 4 0 0 0
    -0.7071 -0.7071 0

doc/src/Howto_spc.rst

@@ -19,7 +19,7 @@ atoms and the water molecule to run a rigid SPC model.
 | LJ :math:`\sigma` of OO = 3.166
 | LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
 | :math:`r_0` of OH bond = 1.0
-| :math:`\theta` of HOH angle = 109.47\ :math:`^{\circ}`
+| :math:`\theta_0` of HOH angle = 109.47\ :math:`^{\circ}`
 |
 
 Note that as originally proposed, the SPC model was run with a 9

doc/src/Howto_structured_data.rst

@@ -184,7 +184,7 @@ frame.
 
 .. code-block:: python
 
-   import re, yaml
+   import yaml
    import pandas as pd
 
    try:
@@ -193,7 +193,7 @@ frame.
        from yaml import SafeLoader as Loader
 
    with open("ave.yaml") as f:
-       ave = yaml.load(docs, Loader=Loader)
+       ave = yaml.load(f, Loader=Loader)
 
    keys = ave['keywords']
    df = {}

doc/src/Intro_citing.rst

@@ -30,8 +30,8 @@ initial versions of LAMMPS is:
   `S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <http://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf>`_
 
 
-DOI for the LAMMPS code
-^^^^^^^^^^^^^^^^^^^^^^^
+DOI for the LAMMPS source code
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 LAMMPS developers use the `Zenodo service at CERN <https://zenodo.org/>`_
 to create digital object identifies (DOI) for stable releases of the

doc/src/Packages_details.rst

@@ -657,7 +657,7 @@ advection-diffusion-reaction systems. The equations of motion of these
 DPD extensions are integrated through a modified velocity-Verlet (MVV)
 algorithm.
 
-**Author:** Zhen Li (Division of Applied Mathematics, Brown University)
+**Author:** Zhen Li (Department of Mechanical Engineering, Clemson University)
 
 **Supporting info:**
 

doc/src/Speed_measure.rst

@@ -42,5 +42,4 @@ inaccurate relative timing data, because processors have to wait when
 communication occurs for other processors to catch up.  Thus the
 reported times for "Communication" or "Other" may be higher than they
 really are, due to load-imbalance.  If this is an issue, you can
-uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile
-LAMMPS, to obtain synchronized timings.
+use the :doc:`timer sync <timer>` command to obtain synchronized timings.

doc/src/Tools.rst

@@ -56,6 +56,7 @@ Pre-processing tools
    * :ref:`moltemplate <moltemplate>`
    * :ref:`msi2lmp <msi>`
    * :ref:`polybond <polybond>`
+   * :ref:`stl_bin2txt <stlconvert>`
 
 
 Post-processing tools
@@ -94,7 +95,7 @@ Miscellaneous tools
    * :ref:`LAMMPS shell <lammps_shell>`
    * :ref:`LAMMPS magic patterns for file(1) <magic>`
    * :ref:`Offline build tool <offline>`
-   * :ref:`singularity <singularity_tool>`
+   * :ref:`singularity/apptainer <singularity_tool>`
    * :ref:`SWIG interface <swig>`
    * :ref:`vim <vim>`
 
@@ -1006,14 +1007,37 @@ Ivanov, at University of Iceland (ali5 at hi.is).
 
 .. _singularity_tool:
 
-singularity tool
-----------------------------------------
+singularity/apptainer tool
+--------------------------
 
-The singularity sub-directory contains container definitions files
-that can be used to build container images for building and testing
-LAMMPS on specific OS variants using the `Singularity <https://sylabs.io>`_
-container software. Contributions for additional variants are welcome.
-For more details please see the README.md file in that folder.
+The singularity sub-directory contains container definitions files that
+can be used to build container images for building and testing LAMMPS on
+specific OS variants using the `Apptainer <https://apptainer.org>`_ or
+`Singularity <https://sylabs.io>`_ container software. Contributions for
+additional variants are welcome.  For more details please see the
+README.md file in that folder.
+
+----------
+
+.. _stlconvert:
+
+stl_bin2txt tool
+----------------
+
+The file stl_bin2txt.cpp converts binary STL files - like they are
+frequently offered for download on the web - into ASCII format STL files
+that LAMMPS can read with the :doc:`create_atoms mesh <create_atoms>` or
+the :doc:`fix smd/wall_surface <fix_smd_wall_surface>` commands.  The syntax
+for running the tool is
+
+.. code-block:: bash
+
+   stl_bin2txt infile.stl outfile.stl
+
+which creates outfile.stl from infile.stl.  This tool must be compiled
+on a platform compatible with the byte-ordering that was used to create
+the binary file.  This usually is a so-called little endian hardware
+(like x86).
 
 ----------
 

doc/src/angle_style.rst

@@ -87,7 +87,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
 * :doc:`dipole <angle_dipole>` - angle that controls orientation of a point dipole
 * :doc:`fourier <angle_fourier>` - angle with multiple cosine terms
 * :doc:`fourier/simple <angle_fourier_simple>` - angle with a single cosine term
-* :doc:`gaussian <angle_gaussian>` - multicentered Gaussian-based angle potential
+* :doc:`gaussian <angle_gaussian>` - multi-centered Gaussian-based angle potential
 * :doc:`harmonic <angle_harmonic>` - harmonic angle
 * :doc:`mm3 <angle_mm3>` - anharmonic angle
 * :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms

doc/src/compute_ave_sphere_atom.rst

@@ -35,16 +35,24 @@ Examples
 Description
 """""""""""
 
-Define a computation that calculates the local density and temperature
-for each atom and neighbors inside a spherical cutoff.
+Define a computation that calculates the local mass density and
+temperature for each atom based on its neighbors inside a spherical
+cutoff.  If an atom has M neighbors, then its local mass density is
+calculated as the sum of its mass and its M neighbor masses, divided
+by the volume of the cutoff sphere (or circle in 2d).  The local
+temperature of the atom is calculated as the temperature of the
+collection of M+1 atoms, after subtracting the center-of-mass velocity
+of the M+1 atoms from each of the M+1 atom's velocities.  This is
+effectively the thermal velocity of the neighborhood of the central
+atom, similar to :doc:`compute temp/com <compute_temp_com>`.
 
-The optional keyword *cutoff* defines the distance cutoff
-used when searching for neighbors. The default value is the cutoff
-specified by the pair style. If no pair style is defined, then a cutoff
-must be defined using this keyword. If the specified cutoff is larger than
-that of the pair_style plus neighbor skin (or no pair style is defined),
-the *comm_modify cutoff* option must also be set to match that of the
-*cutoff* keyword.
+The optional keyword *cutoff* defines the distance cutoff used when
+searching for neighbors. The default value is the cutoff specified by
+the pair style. If no pair style is defined, then a cutoff must be
+defined using this keyword. If the specified cutoff is larger than
+that of the pair_style plus neighbor skin (or no pair style is
+defined), the *comm_modify cutoff* option must also be set to match
+that of the *cutoff* keyword.
 
 The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
@@ -55,16 +63,16 @@ too frequently.
 
    If you have a bonded system, then the settings of
    :doc:`special_bonds <special_bonds>` command can remove pairwise
-   interactions between atoms in the same bond, angle, or dihedral.  This
-   is the default setting for the :doc:`special_bonds <special_bonds>`
-   command, and means those pairwise interactions do not appear in the
-   neighbor list.  Because this fix uses the neighbor list, it also means
-   those pairs will not be included in the order parameter.  This
-   difficulty can be circumvented by writing a dump file, and using the
-   :doc:`rerun <rerun>` command to compute the order parameter for
-   snapshots in the dump file.  The rerun script can use a
-   :doc:`special_bonds <special_bonds>` command that includes all pairs in
-   the neighbor list.
+   interactions between atoms in the same bond, angle, or dihedral.
+   This is the default setting for the :doc:`special_bonds
+   <special_bonds>` command, and means those pairwise interactions do
+   not appear in the neighbor list.  Because this compute uses the
+   neighbor list, it also means those pairs will not be included in
+   the order parameter.  This difficulty can be circumvented by
+   writing a dump file, and using the :doc:`rerun <rerun>` command to
+   compute the order parameter for snapshots in the dump file.  The
+   rerun script can use a :doc:`special_bonds <special_bonds>` command
+   that includes all pairs in the neighbor list.
 
 ----------
 
@@ -77,17 +85,20 @@ too frequently.
 Output info
 """""""""""
 
-This compute calculates a per-atom array with two columns: density and temperature.
+This compute calculates a per-atom array with two columns: mass
+density in density :doc:`units <units>` and temperature in temperature
+:doc:`units <units>`.
 
 These values can be accessed by any command that uses per-atom values
-from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
-page for an overview of LAMMPS output options.
+from a compute as input.  See the :doc:`Howto output <Howto_output>`
+doc page for an overview of LAMMPS output options.
 
 Restrictions
 """"""""""""
 
-This compute is part of the EXTRA-COMPUTE package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+This compute is part of the EXTRA-COMPUTE package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""
@@ -97,5 +108,5 @@ Related commands
 Default
 """""""
 
-The option defaults are *cutoff* = pair style cutoff
+The option defaults are *cutoff* = pair style cutoff.
 

doc/src/create_atoms.rst

@@ -11,7 +11,7 @@ Syntax
    create_atoms type style args keyword values ...
 
 * type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)
-* style = *box* or *region* or *single* or *random*
+* style = *box* or *region* or *single* or *mesh* or *random*
 
   .. parsed-literal::
 
@@ -20,17 +20,19 @@ Syntax
          region-ID = particles will only be created if contained in the region
        *single* args = x y z
          x,y,z = coordinates of a single particle (distance units)
+       *mesh* args = STL-file
+         STL-file = file with triangle mesh in STL format
        *random* args = N seed region-ID
          N = number of particles to create
          seed = random # seed (positive integer)
          region-ID = create atoms within this region, use NULL for entire simulation box
 
 * zero or more keyword/value pairs may be appended
-* keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *units*
+* keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *overlap* or *maxtry* or *units*
 
   .. parsed-literal::
 
-       *mol* value = template-ID seed
+       *mol* values = template-ID seed
          template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
          seed = random # seed (positive integer)
        *basis* values = M itype
@@ -47,9 +49,21 @@ Syntax
        *set* values = dim name
          dim = *x* or *y* or *z*
          name = name of variable to set with x, y, or z atom position
+       *radscale* value = factor
+         factor = scale factor for setting atom radius
+       *meshmode* values = mode arg
+         mode = *bisect* or *qrand*
+         *bisect* arg = radthresh
+           radthresh = threshold value for *mesh* to determine when to split triangles (distance units)
+         *qrand* arg = density
+           density = minimum number density for atoms place on *mesh* triangles (inverse distance squared units)
        *rotate* values = theta Rx Ry Rz
          theta = rotation angle for single molecule (degrees)
          Rx,Ry,Rz = rotation vector for single molecule
+       *overlap* value = Doverlap
+         Doverlap = only insert if at least this distance from all existing atoms
+       *maxtry* value = Ntry
+         Ntry = number of attempts to insert a particle before failure
        *units* value = *lattice* or *box*
          *lattice* = the geometry is defined in lattice units
          *box* = the geometry is defined in simulation box units
@@ -64,17 +78,21 @@ Examples
    create_atoms 3 region regsphere basis 2 3 ratio 0.5 74637
    create_atoms 3 single 0 0 5
    create_atoms 1 box var v set x xpos set y ypos
+   create_atoms 2 random 50 12345 NULL overlap 2.0 maxtry 50
+   create_atoms 1 mesh open_box.stl meshmode qrand 0.1 units box
+   create_atoms 1 mesh funnel.stl meshmode bisect 4.0 units box radscale 0.9
 
 Description
 """""""""""
 
-This command creates atoms (or molecules) on a lattice, or a single
-atom (or molecule), or a random collection of atoms (or molecules), as
-an alternative to reading in their coordinates explicitly via a
-:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
-command.  A simulation box must already exist, which is typically
-created via the :doc:`create_box <create_box>` command.  Before using
-this command, a lattice must also be defined using the
+This command creates atoms (or molecules) within the simulation box,
+either on a lattice, or a single atom (or molecule), or on a surface
+defined by a triangulated mesh, or a random collection of atoms (or
+molecules).  It is an alternative to reading in atom coordinates
+explicitly via a :doc:`read_data <read_data>` or :doc:`read_restart
+<read_restart>` command.  A simulation box must already exist, which is
+typically created via the :doc:`create_box <create_box>` command.
+Before using this command, a lattice must also be defined using the
 :doc:`lattice <lattice>` command, unless you specify the *single* style
 with units = box or the *random* style.  For the remainder of this doc
 page, a created atom or molecule is referred to as a "particle".
@@ -97,58 +115,126 @@ particular dimension, LAMMPS is careful to put exactly one particle at
 the boundary (on either side of the box), not zero or two.
 
 For the *region* style, a geometric volume is filled with particles on
-the lattice.  This volume what is inside the simulation box and is
-also consistent with the region volume.  See the :doc:`region <region>`
-command for details.  Note that a region can be specified so that its
-"volume" is either inside or outside a geometric boundary.  Also note
-that if your region is the same size as a periodic simulation box (in
-some dimension), LAMMPS does not implement the same logic described
-above as for the *box* style, to insure exactly one particle at
-periodic boundaries.  if this is what you desire, you should either
-use the *box* style, or tweak the region size to get precisely the
-particles you want.
+the lattice.  This volume is what is both inside the simulation box
+and also consistent with the region volume.  See the :doc:`region
+<region>` command for details.  Note that a region can be specified so
+that its "volume" is either inside or outside its geometric boundary.
+Also note that if a region is the same size as a periodic simulation
+box (in some dimension), LAMMPS does NOT implement the same logic
+described above for the *box* style, to insure exactly one particle at
+periodic boundaries.  If this is desired, you should either use the
+*box* style, or tweak the region size to get precisely the particles
+you want.
 
 For the *single* style, a single particle is added to the system at
 the specified coordinates.  This can be useful for debugging purposes
 or to create a tiny system with a handful of particles at specified
 positions.
 
-For the *random* style, N particles are added to the system at
-randomly generated coordinates, which can be useful for generating an
-amorphous system.  The particles are created one by one using the
-specified random number *seed*, resulting in the same set of particles
-coordinates, independent of how many processors are being used in the
-simulation.  If the *region-ID* argument is specified as NULL, then
-the created particles will be anywhere in the simulation box.  If a
-*region-ID* is specified, a geometric volume is filled which is both
-inside the simulation box and is also consistent with the region
-volume.  See the :doc:`region <region>` command for details.  Note that
-a region can be specified so that its "volume" is either inside or
-outside a geometric boundary.
+.. figure:: img/marble_race.jpg
+            :figwidth: 33%
+            :align: right
+            :target: _images/marble_race.jpg
+
+For the *mesh* style, a file with a triangle mesh in `STL format
+<https://en.wikipedia.org/wiki/STL_(file_format)>`_ is read and one or
+more particles are placed into the area of each triangle.  The reader
+supports both ASCII and binary files conforming to the format on the
+Wikipedia page.  Binary STL files (e.g. as frequently offered for
+3d-printing) can also be first converted to ASCII for editing with the
+:ref:`stl_bin2txt tool <stlconvert>`.  The use of the *units box* option
+is required. There are two algorithms available for placing atoms:
+*bisect* and *qrand*. They can be selected via the *meshmode* option;
+*bisect* is the default.  If the atom style allows it, the radius will
+be set to a value depending on the algorithm and the value of the
+*radscale* parameter (see below), and the atoms created from the mesh
+are assigned a new molecule ID.
+
+In *bisect* mode a particle is created at the center of each triangle
+unless the average distance of the triangle vertices from its center is
+larger than the *radthresh* value (default is lattice spacing in
+x-direction).  In case the average distance is over the threshold, the
+triangle is recursively split into two halves along the the longest side
+until the threshold is reached. There will be at least one sphere per
+triangle. The value of *radthresh* is set as an argument to *meshmode
+bisect*.  The average distance of the vertices from the center is also
+used to set the radius.
+
+In *qrand* mode a quasi-random sequence is used to distribute particles
+on mesh triangles using an approach by :ref:`(Roberts) <Roberts2019>`.
+Particles are added to the triangle until the minimum number density is
+met or exceeded such that every triangle will have at least one
+particle.  The minimum number density is set as an argument to the
+*qrand* option.  The radius will be set so that the sum of the area of
+the radius of the particles created in place of a triangle will be equal
+to the area of that triangle.
 
 .. note::
 
-   Particles generated by the *random* style will typically be
-   highly overlapped which will cause many interatomic potentials to
-   compute large energies and forces.  Thus you should either perform an
-   :doc:`energy minimization <minimize>` or run dynamics with :doc:`fix nve/limit <fix_nve_limit>` to equilibrate such a system, before
-   running normal dynamics.
+   The atom placement algorithms in the *mesh* style benefit from meshes
+   where triangles are close to equilateral.  It is therefore
+   recommended to pre-process STL files to optimize the mesh
+   accordingly.  There are multiple open source and commercial software
+   tools available with the capability to generate optimized meshes.
 
-Note that this command adds particles to those that already exist.
-This means it can be used to add particles to a system previously read
-in from a data or restart file.  Or the create_atoms command can be
-used multiple times, to add multiple sets of particles to the
-simulation.  For example, grain boundaries can be created, by
-interleaving create_atoms with :doc:`lattice <lattice>` commands
-specifying different orientations.  By using the create_atoms command
-in conjunction with the :doc:`delete_atoms <delete_atoms>` command,
-reasonably complex geometries can be created, or a protein can be
-solvated with a surrounding box of water molecules.
+.. note::
 
-In all these cases, care should be taken to insure that new atoms do
-not overlap existing atoms inappropriately, especially if molecules
-are being added.  The :doc:`delete_atoms <delete_atoms>` command can be
-used to remove overlapping atoms or molecules.
+   In most cases the atoms created in *mesh* style will become an
+   immobile or rigid object that would not be time integrated or moved
+   by :doc:`fix move <fix_move>` or :doc:`fix rigid <fix_rigid>`.  For
+   computational efficiency *and* to avoid undesired contributions to
+   pressure and potential energy due to close contacts, it is usually
+   beneficial to exclude computing interactions between the created
+   particles using :doc:`neigh_modify exclude <neigh_modify>`.
+
+For the *random* style, *N* particles are added to the system at
+randomly generated coordinates, which can be useful for generating an
+amorphous system.  The particles are created one by one using the
+specified random number *seed*, resulting in the same set of particle
+coordinates, independent of how many processors are being used in the
+simulation.  Unless the *overlap* keyword is specified, particles
+created by the *random* style will typically be highly overlapped.
+Various additional criteria can be used to accept or reject a random
+particle insertion; see the keyword discussion below.  Multiple
+attempts per particle are made (see the *maxtry* keyword) until the
+insertion is either successful or fails.  If this command fails to add
+all requested *N* particles, a warning will be output.
+
+If the *region-ID* argument is specified as NULL, then the randomly
+created particles will be anywhere in the simulation box.  If a
+*region-ID* is specified, a geometric volume is filled which is both
+inside the simulation box and is also consistent with the region
+volume.  See the :doc:`region <region>` command for details.  Note
+that a region can be specified so that its "volume" is either inside
+or outside its geometric boundary.
+
+Note that the create_atoms command adds particles to those that
+already exist.  This means it can be used to add particles to a system
+previously read in from a data or restart file.  Or the create_atoms
+command can be used multiple times, to add multiple sets of particles
+to the simulation.  For example, grain boundaries can be created, by
+interleaving the create_atoms command with :doc:`lattice <lattice>`
+commands specifying different orientations.
+
+When this command is used, care should be taken to insure the
+resulting system does not contain particles which are highly
+overlapped.  Such overlaps will cause many interatomic potentials to
+compute huge energies and forces, leading to bad dynamics.  There are
+several strategies to avoid this problem:
+
+* Use the :doc:`delete_atoms overlap <delete_atoms>` command after
+  create_atoms.  For example, this strategy can be used to overlay and
+  surround a large protein molecule with a volume of water molecules,
+  then delete water molecules that overlap with the protein atoms.
+
+* For the *random* style, use the optional *overlap* keyword to avoid
+  overlaps when each new particle is created.
+
+* Before running dynamics on an overlapped system, perform an
+  :doc:`energy minimization <minimize>`.  Or run initial dynamics with
+  :doc:`pair_style soft <pair_soft>` or with :doc:`fix nve/limit
+  <fix_nve_limit>` to un-overlap the particles, before running normal
+  dynamics.
 
 .. note::
 
@@ -156,12 +242,13 @@ used to remove overlapping atoms or molecules.
    that are outside the simulation box; they will just be ignored by
    LAMMPS.  This is true even if you are using shrink-wrapped box
    boundaries, as specified by the :doc:`boundary <boundary>` command.
-   However, you can first use the :doc:`change_box <change_box>` command to
-   temporarily expand the box, then add atoms via create_atoms, then
-   finally use change_box command again if needed to re-shrink-wrap the
-   new atoms.  See the :doc:`change_box <change_box>` page for an
-   example of how to do this, using the create_atoms *single* style to
-   insert a new atom outside the current simulation box.
+   However, you can first use the :doc:`change_box <change_box>`
+   command to temporarily expand the box, then add atoms via
+   create_atoms, then finally use change_box command again if needed
+   to re-shrink-wrap the new atoms.  See the :doc:`change_box
+   <change_box>` doc page for an example of how to do this, using the
+   create_atoms *single* style to insert a new atom outside the
+   current simulation box.
 
 ----------
 
@@ -180,17 +267,19 @@ Using a lattice to add molecules, e.g. via the *box* or *region* or
 points, except that entire molecules are added at each point, i.e. on
 the point defined by each basis atom in the unit cell as it tiles the
 simulation box or region.  This is done by placing the geometric
-center of the molecule at the lattice point, and giving the molecule a
-random orientation about the point.  The random *seed* specified with
-the *mol* keyword is used for this operation, and the random numbers
-generated by each processor are different.  This means the coordinates
-of individual atoms (in the molecules) will be different when running
-on different numbers of processors, unlike when atoms are being
-created in parallel.
+center of the molecule at the lattice point, and (by default) giving
+the molecule a random orientation about the point.  The random *seed*
+specified with the *mol* keyword is used for this operation, and the
+random numbers generated by each processor are different.  This means
+the coordinates of individual atoms (in the molecules) will be
+different when running on different numbers of processors, unlike when
+atoms are being created in parallel.
 
-Also note that because of the random rotations, it may be important to
-use a lattice with a large enough spacing that adjacent molecules will
-not overlap, regardless of their relative orientations.
+Note that with random rotations, it may be important to use a lattice
+with a large enough spacing that adjacent molecules will not overlap,
+regardless of their relative orientations.  See the description of the
+*rotate* keyword below, which overrides the default random orientation
+and inserts all molecules at a specified orientation.
 
 .. note::
 
@@ -204,7 +293,7 @@ not overlap, regardless of their relative orientations.
 
 ----------
 
-This is the meaning of the other allowed keywords.
+This is the meaning of the other optional keywords.
 
 The *basis* keyword is only used when atoms (not molecules) are being
 created.  It specifies an atom type that will be assigned to specific
@@ -234,18 +323,24 @@ and no particle is created if its position is outside the box.
 
 The *var* and *set* keywords can be used together to provide a
 criterion for accepting or rejecting the addition of an individual
-atom, based on its coordinates.  The *name* specified for the *var*
-keyword is the name of an :doc:`equal-style variable <variable>` which
-should evaluate to a zero or non-zero value based on one or two or
-three variables which will store the x, y, or z coordinates of an atom
-(one variable per coordinate).  If used, these other variables must be
-:doc:`internal-style variables <variable>` defined in the input script;
-their initial numeric value can be anything.  They must be
+atom, based on its coordinates.  They apply to all styles except
+*single*.  The *name* specified for the *var* keyword is the name of
+an :doc:`equal-style variable <variable>` which should evaluate to a
+zero or non-zero value based on one or two or three variables which
+will store the x, y, or z coordinates of an atom (one variable per
+coordinate).  If used, these other variables must be
+:doc:`internal-style variables <variable>` defined in the input
+script; their initial numeric value can be anything.  They must be
 internal-style variables, because this command resets their values
 directly.  The *set* keyword is used to identify the names of these
 other variables, one variable for the x-coordinate of a created atom,
 one for y, and one for z.
 
+.. figure:: img/sinusoid.jpg
+            :figwidth: 50%
+            :align: right
+            :target: _images/sinusoid.jpg
+
 When an atom is created, its x,y,z coordinates become the values for
 any *set* variable that is defined.  The *var* variable is then
 evaluated.  If the returned value is 0.0, the atom is not created.  If
@@ -259,28 +354,26 @@ the sinusoid would appear to be "smoother".  Also note the use of the
 "xlat" and "ylat" :doc:`thermo_style <thermo_style>` keywords which
 converts lattice spacings to distance.
 
+.. only:: html
+
+   (Click on the image for a larger version)
+
 .. code-block:: LAMMPS
 
-   dimension       2
-   variable        x equal 100
-   variable        y equal 25
-   lattice         hex 0.8442
-   region          box block 0 $x 0 $y -0.5 0.5
-   create_box      1 box
+   dimension   2
+   variable    x equal 100
+   variable    y equal 25
+   lattice     hex 0.8442
+   region      box block 0 $x 0 $y -0.5 0.5
+   create_box  1 box
 
-   variable        xx internal 0.0
-   variable        yy internal 0.0
-   variable        v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
-   create_atoms    1 box var v set x xx set y yy
-   write_dump      all atom sinusoid.lammpstrj
+   variable    xx internal 0.0
+   variable    yy internal 0.0
+   variable    v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
+   create_atoms  1 box var v set x xx set y yy
+   write_dump  all atom sinusoid.lammpstrj
 
-.. image:: img/sinusoid.jpg
-   :scale: 50%
-   :align: center
-
-.. raw:: html
-
-   Click on the image for a larger version.
+-----
 
 The *rotate* keyword allows specification of the orientation
 at which molecules are inserted.  The axis of rotation is
@@ -291,10 +384,79 @@ the atoms around the rotation axis is consistent with the right-hand
 rule: if your right-hand's thumb points along *R*, then your fingers
 wrap around the axis in the direction of rotation.
 
+The *radscale* keyword only applies to the *mesh* style and adjusts the
+radius of created particles (see above), provided this is supported by
+the atom style.  Its value is a prefactor (must be > 0.0, default is
+1.0) that is applied to the atom radius inferred from the size of the
+individual triangles in the triangle mesh that the particle corresponds
+to.
+
+The *overlap* keyword only applies to the *random* style.  It prevents
+newly created particles from being created closer than the specified
+*Doverlap* distance from any other particle.  When the particles being
+created are molecules, the radius of the molecule (from its geometric
+center) is added to *Doverlap*.  If particles have finite size (see
+:doc:`atom_style sphere <atom_style>` for example) *Doverlap* should
+be specified large enough to include the particle size in the
+non-overlapping criterion.
+
+.. note::
+
+   Checking for overlaps is a costly O(N(N+M)) operation for inserting
+   *N* new particles into a system with *M* existing particles.  This
+   is because distances to all *M* existing particles are computed for
+   each new particle that is added.  Thus the intended use of this
+   keyword is to add relatively small numbers of particles to systems
+   which remain at a relatively low density even after the new
+   particles are created.  Careful use of the *maxtry* keyword in
+   combination with *overlap* is recommended.  See the discussion
+   above about systems with overlapped particles for alternate
+   strategies that allow for overlapped insertions.
+
+The *maxtry* keyword only applies to the *random* style.  It limits
+the number of attempts to generate valid coordinates for a single new
+particle that satisfy all requirements imposed by the *region*, *var*,
+and *overlap* keywords.  The default is 10 attempts per particle
+before the loop over the requested *N* particles advances to the next
+particle.  Note that if insertion success is unlikely (e.g. inserting
+new particles into a dense system using the *overlap* keyword),
+setting the *maxtry* keyword to a large value may result in this
+command running for a long time.
+
+.. figure:: img/overlap.png
+            :figwidth: 30%
+            :align: right
+            :target: _images/overlap.png
+
+Here is an example for the *random* style using these commands
+
+.. code-block:: LAMMPS
+
+   units         lj
+   dimension     2
+   region        box block 0 50 0 50 -0.5 0.5
+   create_box    1 box
+   create_atoms  1 random 2000 13487 NULL overlap 1.0 maxtry 50
+   pair_style    lj/cut 2.5
+   pair_coeff    1 1 1.0 1.0 2.5
+
+to produce a system as shown in the image with 1520 particles (out of
+2000 requested) that are moderately dense and which have no overlaps
+sufficient to prevent the LJ pair_style from running properly (because
+the overlap criterion = 1.0).  The create_atoms command ran for 0.3 s
+on a single CPU core.
+
+.. only:: html
+
+   (Click on the image for a larger version)
+
+-----
+
 The *units* keyword determines the meaning of the distance units used
 to specify the coordinates of the one particle created by the *single*
-style.  A *box* value selects standard distance units as defined by
-the :doc:`units <units>` command, e.g. Angstroms for units = real or
+style, or the overlap distance *Doverlap* by the *overlap* keyword.  A
+*box* value selects standard distance units as defined by the
+:doc:`units <units>` command, e.g. Angstroms for units = real or
 metal.  A *lattice* value means the distance units are in lattice
 spacings.
 
@@ -315,9 +477,10 @@ assigned to created molecules in a similar fashion.
 
 Aside from their ID, atom type, and xyz position, other properties of
 created atoms are set to default values, depending on which quantities
-are defined by the chosen :doc:`atom style <atom_style>`.  See the :doc:`atom style <atom_style>` command for more details.  See the
-:doc:`set <set>` and :doc:`velocity <velocity>` commands for info on how
-to change these values.
+are defined by the chosen :doc:`atom style <atom_style>`.  See the
+:doc:`atom style <atom_style>` command for more details.  See the
+:doc:`set <set>` and :doc:`velocity <velocity>` commands for info on
+how to change these values.
 
 * charge = 0.0
 * dipole moment magnitude = 0.0
@@ -336,9 +499,11 @@ values specified in the file read by the :doc:`molecule <molecule>`
 command.  E.g. the file typically defines bonds (angles,etc) between
 atoms in the molecule, and can optionally define charges on each atom.
 
-Note that the *sphere* atom style sets the default particle diameter
-to 1.0 as well as the density.  This means the mass for the particle
-is not 1.0, but is PI/6 \* diameter\^3 = 0.5236.
+Note that the *sphere* atom style sets the default particle diameter to
+1.0 as well as the density.  This means the mass for the particle is not
+1.0, but is PI/6 \* diameter\^3 = 0.5236.  When using the *mesh* style,
+the particle diameter is adjusted from the size of the individual
+triangles in the triangle mesh.
 
 Note that the *ellipsoid* atom style sets the default particle shape
 to (0.0 0.0 0.0) and the density to 1.0 which means it is a point
@@ -372,5 +537,13 @@ Default
 
 The default for the *basis* keyword is that all created atoms are
 assigned the argument *type* as their atom type (when single atoms are
-being created).  The other defaults are *remap* = no, *rotate* =
-random, and *units* = lattice.
+being created).  The other defaults are *remap* = no, *rotate* = random,
+*radscale* = 1.0, *radthresh* = x-lattice spacing, *overlap* not
+checked, *maxtry* = 10, and *units* = lattice.
+
+----------
+
+.. _Roberts2019:
+
+**(Roberts)** R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning.
+`<http://extremelearning.com.au/evenly-distributing-points-in-a-triangle/>`_

doc/src/delete_atoms.rst

@@ -10,7 +10,7 @@ Syntax
 
    delete_atoms style args keyword value ...
 
-* style = *group* or *region* or *overlap* or *porosity* or *variable*
+* style = *group* or *region* or *overlap* or *random* or *variable*
 
   .. parsed-literal::
 
@@ -20,11 +20,17 @@ Syntax
          cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
          group1-ID = one atom in pair must be in this group
          group2-ID = other atom in pair must be in this group
-       *porosity* args = group-ID region-ID fraction seed
+       *random* args = ranstyle value eflag group-ID region-ID seed
+         ranstyle = *fraction* or *count*
+           for *fraction*:
+             value = fraction (0.0 to 1.0) of eligible atoms to delete
+             eflag =  *no* for fast approximate deletion, *yes* for exact deletion
+           for *count*:
+             value = number of atoms to delete
+             eflag = *no* for warning if count > eligible atoms, *yes* for error
          group-ID = group within which to perform deletions
          region-ID = region within which to perform deletions
                      or NULL to only impose the group criterion
-         fraction = delete this fraction of atoms
          seed = random number seed (positive integer)
        *variable* args = variable-name
 
@@ -46,16 +52,17 @@ Examples
    delete_atoms region sphere compress no
    delete_atoms overlap 0.3 all all
    delete_atoms overlap 0.5 solvent colloid
-   delete_atoms porosity all cube 0.1 482793 bond yes
-   delete_atoms porosity polymer cube 0.1 482793 bond yes
+   delete_atoms random fraction 0.1 yes all cube 482793 bond yes
+   delete_atoms random fraction 0.3 no polymer NULL 482793 bond yes
+   delete_atoms random count 500 no ions NULL 482793
    detele_atoms variable checkers
 
 Description
 """""""""""
 
-Delete the specified atoms.  This command can be used to carve out
-voids from a block of material or to delete created atoms that are too
-close to each other (e.g. at a grain boundary).
+Delete the specified atoms.  This command can be used, for example, to
+carve out voids from a block of material or to delete created atoms
+that are too close to each other (e.g. at a grain boundary).
 
 For style *group*, all atoms belonging to the group are deleted.
 
@@ -81,17 +88,33 @@ have occurred that no atom pairs within the cutoff will remain
 minimum number of atoms will be deleted, or that the same atoms will
 be deleted when running on different numbers of processors.
 
-For style *porosity* a specified *fraction* of atoms are deleted which
-are both in the specified group and within the specified region.  The
-region-ID can be specified as NULL to only impose the group criterion.
-Likewise, specifying the group-ID as *all* will only impose the region
-criterion.
+For style *random* a subset of eligible atoms are deleted.  Which
+atoms to delete are chosen randomly using the specified random number
+*seed*.  Which atoms are deleted may vary when running on different
+numbers of processors.
 
-For example, if fraction is 0.1, then 10% of the eligible atoms will
-be deleted.  The atoms to delete are chosen randomly.  There is no
-guarantee that the exact fraction of atoms will be deleted, or that
-the same atoms will be deleted when running on different numbers of
-processors.
+For *ranstyle* = *fraction*, the specified fractional *value* (0.0 to
+1.0) of eligible atoms are deleted.  If *eflag* is set to *no*, then
+the number of deleted atoms will be approximate, but the operation
+will be fast.  If *eflag* is set to *yes*, then the number deleted
+will match the requested fraction, but for large systems the selection
+of deleted atoms may take additional time to determine.
+
+For *ranstyle* = *count*, the specified integer *value* is the number
+of eligible atoms are deleted.  If *eflag* is set to *no*, then if the
+requested number is larger then the number of eligible atoms, a
+warning is issued and only the eligible atoms are deleted instead of
+the requested *value*.  If *eflag* is set to *yes*, an error is
+triggered instead and LAMMPS will exit.  For large systems the
+selection of atoms to delete may take additional time to determine,
+the same as for requesting an exact fraction with *pstyle* =
+*fraction*.
+
+Which atoms are eligible for deletion for style *random* is determined
+by the specified *group-ID* and *region-ID*.  To be eligible, an atom
+must be in both the specified group and region.  If *group-ID* = all,
+there is effectively no group criterion.  If *region-ID* is specified
+as NULL, no region criterion is imposed.
 
 For style *variable*, all atoms for which the atom-style variable with
 the given name evaluates to non-zero will be deleted. Additional atoms
@@ -100,6 +123,10 @@ were deleted within the region; see the *mol* keyword discussion below.
 This option allows complex selections of atoms not covered by the
 other options listed above.
 
+----------
+
+Here is the meaning of the optional keywords.
+
 If the *compress* keyword is set to *yes*, then after atoms are
 deleted, then atom IDs are re-assigned so that they run from 1 to the
 number of atoms in the system.  Note that this is not done for

doc/src/dump.rst

@@ -133,13 +133,14 @@ Examples
 
 .. code-block:: LAMMPS
 
-   dump myDump all atom 100 dump.atom
+   dump myDump all atom 100 dump.lammpstrj
    dump myDump all atom/mpiio 100 dump.atom.mpiio
    dump myDump all atom/gz 100 dump.atom.gz
    dump myDump all atom/zstd 100 dump.atom.zst
    dump 2 subgroup atom 50 dump.run.bin
    dump 2 subgroup atom/mpiio 50 dump.run.mpiio.bin
    dump 4a all custom 100 dump.myforce.* id type x y vx fx
+   dump 4a all custom 100 dump.myvel.lammpsbin id type x y z vx vy vz
    dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
    dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
    dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
@@ -419,6 +420,7 @@ style.
 .. code-block:: yaml
 
    ---
+   creator: LAMMPS
    timestep: 0
    units: lj
    time: 0
@@ -534,11 +536,11 @@ MPI-IO.
 Note that MPI-IO dump files are one large file which all processors
 write to.  You thus cannot use the "%" wildcard character described
 above in the filename since that specifies generation of multiple
-files.  You can use the ".bin" suffix described below in an MPI-IO
+files.  You can use the ".bin" or ".lammpsbin" suffix described below in an MPI-IO
 dump file; again this file will be written in parallel and have the
 same binary format as if it were written without MPI-IO.
 
-If the filename ends with ".bin", the dump file (or files, if "\*" or
+If the filename ends with ".bin" or ".lammpsbin", the dump file (or files, if "\*" or
 "%" is also used) is written in binary format.  A binary dump file
 will be about the same size as a text version, but will typically
 write out much faster.  Of course, when post-processing, you will need

doc/src/dump_image.rst

@@ -44,7 +44,7 @@ Syntax
          color = *type*
          bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
        *fix* = fixID color fflag1 fflag2
-         fixID = ID of fix that generates objects to dray
+         fixID = ID of fix that generates objects to draw
          color = *type*
          fflag1,fflag2 = 2 numeric flags to affect how fix objects are drawn
        *size* values = width height = size of images

doc/src/dump_modify.rst

@@ -392,9 +392,8 @@ keyword. For *atom* dump styles only the keywords "id", "type", "x",
 "y", "z", "ix", "iy", "iz" can be accessed via string regardless of
 whether scaled or unwrapped coordinates were enabled or disabled, and
 it always assumes 8 columns for indexing regardless of whether image
-flags are enabled or not.  For dump style *cfg* only the "auxiliary"
-keywords (6th or later keyword) may be changed and the column indexing
-considers only them (i.e. the 6th keyword is the the 1st column).
+flags are enabled or not.  For dump style *cfg* only changes to the
+"auxiliary" keywords (6th or later keyword) will become visible.
 
 The *colname* keyword can be used multiple times. If multiple *colname*
 settings refer to the same keyword, the last setting has precedence.  A

doc/src/fix_hyper_local.rst

@@ -75,7 +75,7 @@ doc page.  This description of LHD builds on the GHD description.
 
 The definition of bonds and :math:`E_{ij}` are the same for GHD and LHD.
 The formulas for :math:`V^{max}_{ij}` and :math:`F^{max}_{ij}` are also
-the same except for a pre-factor :math:`C_{ij}`, explained below.
+the same except for a prefactor :math:`C_{ij}`, explained below.
 
 The bias energy :math:`V_{ij}` applied to a bond *ij* with maximum strain is
 
@@ -256,7 +256,7 @@ Note that this fix does not know the *cutevent* parameter, but uses
 half the *cutbond* parameter as an estimate to warn if the ghost
 cutoff is not long enough.
 
-As described above the *alpha* argument is a pre-factor in the
+As described above the *alpha* argument is a prefactor in the
 boostostat update equation for each bond's :math:`C_{ij}` prefactor.
 *Alpha* is specified in time units, similar to other thermostat or barostat
 damping parameters.  It is roughly the physical time it will take the

doc/src/fix_mdi_aimd.rst

@@ -12,7 +12,6 @@ Syntax
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * mdi/aimd = style name of this fix command
-* optional keyword = *plugin*
 
 Examples
 """"""""
@@ -20,7 +19,6 @@ Examples
 .. code-block:: LAMMPS
 
    fix 1 all mdi/aimd
-   fix 1 all mdi/aimd plugin
 
 Description
 """""""""""
@@ -53,14 +51,6 @@ same time as LAMMPS, or as a plugin library.  See the :doc:`mdi plugin
 Again, the examples/mdi/README file explains how to launch both driver
 and engine codes so that engine is used in plugin mode.
 
-To use this fix with a plugin engine, you must specify the
-*plugin* keyword as the last argument, as illustrated above.
-
-.. note::
-
-   As of April 2022, the *plugin* keyword is needed.  In a future
-   version of the MDI library it will no longer be necessary.
-
 ----------
 
 This fix performs the timestepping portion of an AIMD simulation.

doc/src/fix_momentum.rst

@@ -21,7 +21,8 @@ Syntax
 * momentum = style name of this fix command
 * N = adjust the momentum every this many timesteps
   one or more keyword/value pairs may be appended
-* keyword = *linear* or *angular* or *rescale*
+
+.. parsed-literal::
 
    fix ID group-ID momentum/chunk N chunkID keyword values ...
 
@@ -30,7 +31,7 @@ Syntax
 * N = adjust the momentum per chunk every this many timesteps
 * chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
 
-  one or more keyword/value pairs may be appended
+  one or more keyword/value settings may be appended to each of the fix commands:
 * keyword = *linear* or *angular* or *rescale*
 
   .. parsed-literal::

doc/src/fix_print.rst

@@ -39,19 +39,35 @@ Description
 Print a text string every N steps during a simulation run.  This can
 be used for diagnostic purposes or as a debugging tool to monitor some
 quantity during a run.  The text string must be a single argument, so
-it should be enclosed in double quotes if it is more than one word.
-If it contains variables it must be enclosed in double quotes to
-insure they are not evaluated when the input script line is read, but
-will instead be evaluated each time the string is printed.
+it should be enclosed in single or double quotes if it is more than
+one word.  If it contains variables it must be enclosed in double
+quotes to insure they are not evaluated when the input script line is
+read, but will instead be evaluated each time the string is printed.
 
-Instead of a numeric value, N can be specified as an :doc:`equal-style variable <variable>`, which should be specified as v_name, where
-name is the variable name.  In this case, the variable is evaluated at
-the beginning of a run to determine the **next** timestep at which the
+.. note::
+
+   As discussed on the :doc:`Commands parse <Commands_parse>` doc
+   page, the text string can use "immediate" variables, specified as
+   $(formula) with parenthesis, where the numeric formula has the same
+   syntax as equal-style variables described on the :doc:`variable
+   <variable>` doc page.  This is a convenient way to evaluate a
+   formula immediately without using the variable command to define a
+   named variable and then use that variable in the text string.  The
+   formula can include a trailing colon and format string which
+   determines the precision with which the numeric value is output.
+   This is also explained on the :doc:`Commands parse
+   <Commands_parse>` doc page.
+
+Instead of a numeric value, N can be specified as an :doc:`equal-style
+variable <variable>`, which should be specified as v_name, where name
+is the variable name.  In this case, the variable is evaluated at the
+beginning of a run to determine the **next** timestep at which the
 string will be written out.  On that timestep, the variable will be
-evaluated again to determine the next timestep, etc.
-Thus the variable should return timestep values.  See the stagger()
-and logfreq() and stride() math functions for :doc:`equal-style variables <variable>`, as examples of useful functions to use in
-this context. For example, the following commands will print output at
+evaluated again to determine the next timestep, etc.  Thus the
+variable should return timestep values.  See the stagger() and
+logfreq() and stride() math functions for :doc:`equal-style variables
+<variable>`, as examples of useful functions to use in this
+context. For example, the following commands will print output at
 timesteps 10,20,30,100,200,300,1000,2000,etc:
 
 .. code-block:: LAMMPS
@@ -61,12 +77,12 @@ timesteps 10,20,30,100,200,300,1000,2000,etc:
 
 The specified group-ID is ignored by this fix.
 
-See the :doc:`variable <variable>` command for a description of *equal*
-style variables which are the most useful ones to use with the fix
-print command, since they are evaluated afresh each timestep that the
-fix print line is output.  Equal-style variables calculate formulas
-involving mathematical operations, atom properties, group properties,
-thermodynamic properties, global values calculated by a
+See the :doc:`variable <variable>` command for a description of
+*equal* style variables which are the most useful ones to use with the
+fix print command, since they are evaluated afresh each timestep that
+the fix print line is output.  Equal-style variables calculate
+formulas involving mathematical operations, atom properties, group
+properties, thermodynamic properties, global values calculated by a
 :doc:`compute <compute>` or :doc:`fix <fix>`, or references to other
 :doc:`variables <variable>`.
 
@@ -92,11 +108,13 @@ where ID is replaced with the fix-ID.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
-are relevant to this fix.  No global or per-atom quantities are stored
-by this fix for access by various :doc:`output commands <Howto_output>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
+relevant to this fix.  No global or per-atom quantities are stored by
+this fix for access by various :doc:`output commands <Howto_output>`.
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_restrain.rst

@@ -59,7 +59,7 @@ of a bond or angle or dihedral interaction whose strength can vary
 over time during a simulation.  This is functionally similar to
 creating a bond or angle or dihedral for the same atoms in a data
 file, as specified by the :doc:`read_data <read_data>` command, albeit
-with a time-varying pre-factor coefficient, and except for exclusion
+with a time-varying prefactor coefficient, and except for exclusion
 rules, as explained below.
 
 For the purpose of force field parameter-fitting or mapping a molecular

doc/src/fix_wall.rst

@@ -199,7 +199,7 @@ inside the colloid particle and wall.  Note that the cutoff distance Rc
 in this case is the distance from the colloid particle center to the
 wall.  The prefactor :math:`\epsilon` can be thought of as an effective
 Hamaker constant with energy units for the strength of the colloid-wall
-interaction.  More specifically, the :math:`\epsilon` pre-factor is
+interaction.  More specifically, the :math:`\epsilon` prefactor is
 :math:`4\pi^2 \rho_{wall} \rho_{colloid} \epsilon \sigma^6`, where
 :math:`\epsilon` and :math:`\sigma` are the LJ parameters for the
 constituent LJ particles. :math:`\rho_{wall}` and :math:`\rho_{colloid}`
@@ -211,7 +211,7 @@ constituent LJ particles of size :math:`\sigma` within the colloid particle
 and a 3d half-lattice of Lennard-Jones 12/6 particles of size :math:`\sigma`
 in the wall.  As mentioned in the preceding paragraph, the density of
 particles in the wall and colloid can be different, as specified by
-the :math:`\epsilon` pre-factor.
+the :math:`\epsilon` prefactor.
 
 For the *wall/harmonic* style, :math:`\epsilon` is effectively the spring
 constant K, and has units (energy/distance\^2).  The input parameter

doc/src/fix_wall_ees.rst

@@ -88,7 +88,7 @@ examples/ directory.
 The prefactor :math:`\epsilon` can be thought of as an
 effective Hamaker constant with energy units for the strength of the
 ellipsoid-wall interaction.  More specifically, the :math:`\epsilon`
-pre-factor is
+prefactor is
 
 .. math::
 

doc/src/kspace_style.rst

@@ -129,8 +129,8 @@ Examples
 
    kspace_style pppm 1.0e-4
    kspace_style pppm/cg 1.0e-5 1.0e-6
-   kspace style msm 1.0e-4
-   kspace style scafacos fmm 1.0e-4
+   kspace_style msm 1.0e-4
+   kspace_style scafacos fmm 1.0e-4
    kspace_style none
 
 Used in input scripts:
@@ -475,8 +475,8 @@ that package **and** the KSPACE package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
 For MSM, a simulation must be 3d and one can use any combination of
-periodic, non-periodic, or shrink-wrapped boundaries (specified using
-the :doc:`boundary <boundary>` command).
+periodic, non-periodic, but not shrink-wrapped boundaries (specified
+using the :doc:`boundary <boundary>` command).
 
 For Ewald and PPPM, a simulation must be 3d and periodic in all
 dimensions.  The only exception is if the slab option is set with

doc/src/min_spin.rst

@@ -98,6 +98,10 @@ see their implementation reported in :ref:`(Ivanov) <Ivanov1>`.
 Restrictions
 """"""""""""
 
+The *spin*, *spin/cg*, and *spin/lbfgps* styles are part of the SPIN
+package.  They are only enabled if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` page for more info.
+
 This minimization procedure is only applied to spin degrees of
 freedom for a frozen lattice configuration.
 

doc/src/min_style.rst

@@ -1,25 +1,55 @@
 .. index:: min_style
 
-min_style command
-=================
+min_style cg command
+====================
+
+min_style hftn command
+======================
+
+min_style sd command
+====================
+
+min_style quickmin command
+==========================
+
+min_style fire command
+======================
+
+min_style fire/old command
+==========================
+
+:doc:`min_style spin <min_spin>` command
+========================================
+
+:doc:`min_style spin/cg <min_spin>` command
+===========================================
+
+:doc:`min_style spin/lbfgs <min_spin>` command
+==============================================
 
 Syntax
 """"""
 
-.. code-block:: LAMMPS
+.. parsed-literal::
 
    min_style style
 
 * style = *cg* or *hftn* or *sd* or *quickmin* or *fire* or *fire/old* or *spin* or *spin/cg* or *spin/lbfgs*
 
+  .. parsed-literal::
+
+       *spin* is discussed briefly here and fully on :doc:`min_style spin <min_spin>` doc page
+       *spin/cg* is discussed briefly here and fully on :doc:`min_style spin <min_spin>` doc page
+       *spin/lbfgs* is discussed briefly here and fully on :doc:`min_style spin <min_spin>` doc page
+
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
    min_style cg
-   min_style spin
    min_style fire
+   min_style spin
 
 Description
 """""""""""
@@ -124,7 +154,9 @@ calculations via the :doc:`neb/spin <neb_spin>` command.
 Restrictions
 """"""""""""
 
-none
+The *spin*, *spin/cg*, and *spin/lbfgps* styles are part of the SPIN
+package.  They are only enabled if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/pair_e3b.rst

@@ -50,6 +50,12 @@ Examples
    pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.15 8.5
    pair_coeff * * e3b preset 2011
 
+Used in example input script:
+
+.. parsed-literal::
+
+   examples/PACKAGES/e3b/in.e3b-tip4p2005
+
 Description
 """""""""""
 
@@ -68,21 +74,27 @@ The *e3b* style computes an \"explicit three-body\" (E3B) potential for water :r
    0 & r>R_f\\
    \end{cases}
 
-This potential was developed as a water model that includes the three-body cooperativity of hydrogen bonding explicitly.
-To use it in this way, it must be applied in conjunction with a conventional two-body water model, through *pair_style hybrid/overlay*.
-The three body interactions are split into three types: A, B, and C.
-Type A corresponds to anti-cooperative double hydrogen bond donor interactions.
-Type B corresponds to the cooperative interaction of molecules that both donate and accept a hydrogen bond.
-Type C corresponds to anti-cooperative double hydrogen bond acceptor interactions.
-The three-body interactions are smoothly cutoff by the switching function s(r) between Rs and Rc3.
-The two-body interactions are designed to correct for the effective many-body interactions implicitly included in the conventional two-body potential.
-The two-body interactions are cut off sharply at Rc2, because K3 is typically significantly smaller than K2.
-See :ref:`(Kumar 2008) <Kumar>` for more details.
+This potential was developed as a water model that includes the
+three-body cooperativity of hydrogen bonding explicitly.  To use it in
+this way, it must be applied in conjunction with a conventional two-body
+water model, through pair style :doc:`hybrid/overlay <pair_hybrid>`.  The
+three body interactions are split into three types: A, B, and C.  Type A
+corresponds to anti-cooperative double hydrogen bond donor interactions.
+Type B corresponds to the cooperative interaction of molecules that both
+donate and accept a hydrogen bond.  Type C corresponds to
+anti-cooperative double hydrogen bond acceptor interactions.  The
+three-body interactions are smoothly cutoff by the switching function
+s(r) between Rs and Rc3.  The two-body interactions are designed to
+correct for the effective many-body interactions implicitly included in
+the conventional two-body potential.  The two-body interactions are cut
+off sharply at Rc2, because K3 is typically significantly smaller than
+K2.  See :ref:`(Kumar 2008) <Kumar>` for more details.
 
-Only a single *pair_coeff* command is used with the *e3b* style.
-The first two arguments must be \* \*.
-The oxygen atom type for the pair style is passed as the only argument to the *pair_style* command, not in the *pair_coeff* command.
-The hydrogen atom type is inferred by the ordering of the atoms.
+Only a single :doc:`pair_coeff <pair_coeff>` command is used with the
+*e3b* style and the first two arguments must be \* \*.  The oxygen atom
+type for the pair style is passed as the only argument to the
+*pair_style* command, not in the *pair_coeff* command.  The hydrogen
+atom type is inferred from the ordering of the atoms.
 
 .. note::
 
@@ -90,26 +102,41 @@ The hydrogen atom type is inferred by the ordering of the atoms.
    Each water molecule must have consecutive IDs with the oxygen first.
    This pair style does not test that this criteria is met.
 
-The *pair_coeff* command must have at least one keyword/value pair, as described above.
-The *preset* keyword sets the potential parameters to the values used in :ref:`(Tainter 2011) <Tainter2011>` or :ref:`(Tainter 2015) <Tainter2015>`.
-To use the water models defined in those references, the *e3b* style should always be used in conjunction with an *lj/cut/tip4p/long* style through *pair_style hybrid/overlay*, as demonstrated in the second example above.
-The *preset 2011* option should be used with the :doc:`TIP4P water model <Howto_tip4p>`.
-The *preset 2015* option should be used with the :doc:`TIP4P/2005 water model <Howto_tip4p>`.
-If the *preset* keyword is used, no other keyword is needed.
-Changes to the preset parameters can be made by specifying the *preset* keyword followed by the specific parameter to change, like *Ea*\ .
-Note that the other keywords must come after *preset* in the pair_style command.
-The *e3b* style can also be used to implement any three-body potential of the same form by specifying all the keywords except *neigh*\ : *Ea*, *Eb*, *Ec*, *E2*, *K3*, *K2*, *Rc3*, *Rc2*, *Rs*, and *bondL*\ .
-The keyword *bondL* specifies the intramolecular OH bond length of the water model being used.
-This is needed to include H atoms that are within the cutoff even when the attached oxygen atom is not.
+The *pair_coeff* command must have at least one keyword/value pair, as
+described above.  The *preset* keyword sets the potential parameters to
+the values used in :ref:`(Tainter 2011) <Tainter2011>` or
+:ref:`(Tainter 2015) <Tainter2015>`.  To use the water models defined in
+those references, the *e3b* style should always be used in conjunction
+with an *lj/cut/tip4p/long* style through *pair_style hybrid/overlay*,
+as demonstrated in the second example above.  The *preset 2011* option
+should be used with the :doc:`TIP4P water model <Howto_tip4p>`.  The
+*preset 2015* option should be used with the :doc:`TIP4P/2005 water
+model <Howto_tip4p>`.  If the *preset* keyword is used, no other keyword
+is needed.  Changes to the preset parameters can be made by specifying
+the *preset* keyword followed by the specific parameter to change, like
+*Ea*\ .  Note that the other keywords must come after *preset* in the
+pair_style command.  The *e3b* style can also be used to implement any
+three-body potential of the same form by specifying all the keywords
+except *neigh*\ : *Ea*, *Eb*, *Ec*, *E2*, *K3*, *K2*, *Rc3*, *Rc2*,
+*Rs*, and *bondL*\ .  The keyword *bondL* specifies the intramolecular
+OH bond length of the water model being used.  This is needed to include
+H atoms that are within the cutoff even when the attached oxygen atom is
+not.
 
-This pair style allocates arrays sized according to the number of pairwise interactions within Rc3.
-To do this it needs an estimate for the number of water molecules within Rc3 of an oxygen atom.
-This estimate defaults to 10 and can be changed using the *neigh* keyword, which takes an integer as an argument.
-If the neigh setting is too small, the simulation will fail with the error "neigh is too small".
-If the neigh setting is too large, the pair style will use more memory than necessary.
+This pair style allocates arrays sized according to the number of
+pairwise interactions within Rc3.  To do this it needs an estimate for
+the number of water molecules within Rc3 of an oxygen atom.  This
+estimate defaults to 10 and can be changed using the *neigh* keyword,
+which takes an integer as an argument.  If the neigh setting is too
+small, the simulation will fail with the error "neigh is too small".  If
+the neigh setting is too large, the pair style will use more memory than
+necessary.
 
-This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 4.
-The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term.
+This pair style tallies a breakdown of the total E3B potential energy
+into sub-categories, which can be accessed via the :doc:`compute pair
+<compute_pair>` command as a vector of values of length 4.  The 4 values
+correspond to the terms in the first equation above: the E2 term, the Ea
+term, the Eb term, and the Ec term.
 
 See the examples/PACKAGES/e3b directory for a complete example script.
 

doc/src/pair_gran.rst

@@ -144,7 +144,7 @@ two particles, and is thus a non-linear function of overlap distance.
 Thus Kn has units of force per area and is thus specified in units of
 (pressure).  The effects of absolute particle size (monodispersity)
 and relative size (polydispersity) are captured in the radii-dependent
-pre-factors.  When these pre-factors are carried through to the other
+prefactors.  When these prefactors are carried through to the other
 terms in the force equation it means that the specified :math:`\gamma_n` is in
 units of (1/(time\*distance)), :math:`K_t` is in units of (pressure), and
 :math:`\gamma_t` is in units of (1/(time\*distance)).

doc/src/pair_multi_lucy.rst

@@ -54,7 +54,7 @@ form.
 
 An interpolation table is used to evaluate the density-dependent energy
 (:math:`\int A(\rho') d\rho'`) and force (:math:`A(\rho')`).  Note that
-the pre-factor to the energy is computed after the interpolation, thus
+the prefactor to the energy is computed after the interpolation, thus
 the :math:`\int A(\rho') d \rho'` will have units of energy / length\^4.
 
 The interpolation table is created as a pre-computation by fitting

doc/src/pair_multi_lucy_rx.rst

@@ -67,7 +67,7 @@ form.
 
 An interpolation table is used to evaluate the density-dependent energy
 (:math:`\int A(\rho') d \rho'`) and force (:math:`A(\rho')`).  Note that
-the pre-factor to the energy is computed after the interpolation, thus
+the prefactor to the energy is computed after the interpolation, thus
 the :math:`\int A(\rho') d\rho'` will have units of energy / length\^4.
 
 The interpolation table is created as a pre-computation by fitting

doc/src/pair_none.rst

@@ -20,28 +20,37 @@ Examples
 Description
 """""""""""
 
-Using a pair style of none means pair forces and energies are not
-computed.
+Using a pair style of *none* means that any previous pair style setting
+will be deleted and pairwise forces and energies are not computed.
 
-With this choice, the force cutoff is 0.0, which means that only atoms
-within the neighbor skin distance (see the :doc:`neighbor <neighbor>`
-command) are communicated between processors.  You must insure the
-skin distance is large enough to acquire atoms needed for computing
-bonds, angles, etc.
+As a consequence there will be a pairwise force cutoff of 0.0, which has
+implications for the default setting of the neighbor list and the
+communication cutoff.  Those are the sum of the largest pairwise cutoff
+and the neighbor skin distance (see the documentation of the
+:doc:`neighbor <neighbor>` command and the :doc:`comm_modify
+<comm_modify>` command).  When you have bonds, angles, dihedrals, or
+impropers defined at the same time, you must set the communication
+cutoff so that communication cutoff distance is large enough to acquire
+and communicate sufficient ghost atoms from neighboring sub-domains as
+needed for computing bonds, angles, etc.
 
-A pair style of *none* will also prevent pairwise neighbor lists from
-being built.  However if the :doc:`neighbor <neighbor>` style is *bin*,
-data structures for binning are still allocated.  If the neighbor skin
-distance is small, then these data structures can consume a large
-amount of memory.  So you should either set the neighbor style to
-*nsq* or set the skin distance to a larger value.
+A pair style of *none* will also not request a pairwise neighbor list.
+However if the :doc:`neighbor <neighbor>` style is *bin*, data
+structures for binning are still allocated.  If the neighbor list cutoff
+is small, then these data structures can consume a large amount of
+memory.  So you should either set the neighbor style to *nsq* or set the
+skin distance to a larger value.
 
-See the :doc:`pair_style zero <pair_zero>` for a way to trigger the
-building of a neighbor lists, but compute no pairwise interactions.
+See the :doc:`pair_style zero <pair_zero>` for a way to set a pairwise
+cutoff and thus trigger the building of a neighbor lists and setting
+a corresponding communication cutoff, but compute no pairwise interactions.
 
 Restrictions
 """"""""""""
-none
+
+You must not use a :doc:`pair_coeff <pair_coeff>` command with this pair
+style.  Since there is no interaction computed, you cannot set any
+coefficients for it.
 
 Related commands
 """"""""""""""""

doc/src/pair_pace.rst

@@ -1,7 +1,10 @@
 .. index:: pair_style pace
+.. index:: pair_style pace/kk
 
 pair_style pace command
-========================
+=======================
+
+Accelerator Variants: *pace/kk*
 
 Syntax
 """"""
@@ -10,13 +13,14 @@ Syntax
 
    pair_style pace ... keyword values ...
 
-* an optional keyword may be appended
-* keyword = *product* or *recursive*
+* one or more keyword/value pairs may be appended
 
   .. parsed-literal::
 
+     keyword = *product* or *recursive* or *chunksize*
        *product* = use product algorithm for basis functions
        *recursive* = use recursive algorithm for basis functions
+       *chunksize* value = number of atoms in each pass
 
 Examples
 """"""""
@@ -24,7 +28,7 @@ Examples
 .. code-block:: LAMMPS
 
    pair_style pace
-   pair_style pace product
+   pair_style pace product chunksize 2048
    pair_coeff * * Cu-PBE-core-rep.ace Cu
 
 Description
@@ -59,11 +63,19 @@ Note that unlike for other potentials, cutoffs are
 not set in the pair_style or pair_coeff command; they are specified in
 the ACE file.
 
-The pair_style *pace* command may be followed by an optional keyword
+The pair_style *pace* command may be followed by the optional keyword
 *product* or *recursive*, which determines which of two algorithms
 is used for the calculation of basis functions and derivatives.
 The default is *recursive*.
 
+The keyword *chunksize* is only applicable when
+using the pair style *pace* with the KOKKOS package on GPUs and is
+ignored otherwise.  This keyword controls the number of atoms
+in each pass used to compute the atomic cluster expansion and is used to
+avoid running out of memory.  For example if there are 8192 atoms in the
+simulation and the *chunksize* is set to 4096, the ACE
+calculation will be broken up into two passes (running on a single GPU).
+
 See the :doc:`pair_coeff <pair_coeff>` page for alternate ways
 to specify the path for the ACE coefficient file.
 
@@ -88,6 +100,10 @@ This pair style can only be used via the *pair* keyword of the
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Restrictions
 """"""""""""
 
@@ -103,7 +119,7 @@ Related commands
 Default
 """""""
 
-recursive
+recursive, chunksize = 4096
 
 .. _Drautz20191:
 

doc/src/pair_soft.rst

@@ -41,7 +41,7 @@ Style *soft* computes pairwise interactions with the formula
    \qquad r < r_c
 
 It is useful for pushing apart overlapping atoms, since it does not
-blow up as r goes to 0.  A is a pre-factor that can be made to vary in
+blow up as r goes to 0.  A is a prefactor that can be made to vary in
 time from the start to the end of the run (see discussion below),
 e.g. to start with a very soft potential and slowly harden the
 interactions over time.  Rc is the cutoff.  See the :doc:`fix nve/limit <fix_nve_limit>` command for another way to push apart

doc/src/pair_style.rst

@@ -348,6 +348,7 @@ accelerated styles exist.
 * :doc:`spin/neel <pair_spin_neel>` -
 * :doc:`srp <pair_srp>` -
 * :doc:`sw <pair_sw>` - Stillinger-Weber 3-body potential
+* :doc:`sw/angle/table <pair_sw_angle_table>` - Stillinger-Weber potential with tabulated angular term
 * :doc:`sw/mod <pair_sw>` - modified Stillinger-Weber 3-body potential
 * :doc:`table <pair_table>` - tabulated pair potential
 * :doc:`table/rx <pair_table_rx>` -
@@ -358,6 +359,7 @@ accelerated styles exist.
 * :doc:`tersoff/table <pair_tersoff>` -
 * :doc:`tersoff/zbl <pair_tersoff_zbl>` - Tersoff/ZBL 3-body potential
 * :doc:`thole <pair_thole>` - Coulomb interactions with thole damping
+* :doc:`threebody/table <pair_threebody_table>` - generic tabulated three-body potential
 * :doc:`tip4p/cut <pair_coul>` - Coulomb for TIP4P water w/out LJ
 * :doc:`tip4p/long <pair_coul>` - long-range Coulomb for TIP4P water w/out LJ
 * :doc:`tip4p/long/soft <pair_fep_soft>` -

doc/src/pair_sw_angle_table.rst

@@ -0,0 +1,311 @@
+.. index:: pair_style sw/angle/table
+
+pair_style sw/angle/table command
+=================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style style
+
+* style = *sw/angle/table*
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style sw/angle/table
+   pair_coeff * * spce.sw type
+
+Used in example input script:
+
+.. parsed-literal::
+
+   examples/PACKAGES/manybody_table/in.spce_sw
+
+
+Description
+"""""""""""
+
+The *sw/angle/table* style is a modification of the original
+:doc:`pair_style sw <pair_sw>`. It has been developed for coarse-grained
+simulations (of water) (:ref:`Scherer1 <Scherer1>`), but can be employed
+for all kinds of systems. It computes a modified 3-body
+:ref:`Stillinger-Weber <Stillinger3>` potential for the energy E of a
+system of atoms as
+
+.. math::
+
+   E & =  \sum_i \sum_{j > i} \phi_2 (r_{ij}) +
+          \sum_i \sum_{j \neq i} \sum_{k > j}
+          \phi_3 (r_{ij}, r_{ik}, \theta_{ijk}) \\
+  \phi_2(r_{ij}) & =  A_{ij} \epsilon_{ij} \left[ B_{ij} (\frac{\sigma_{ij}}{r_{ij}})^{p_{ij}} -
+                    (\frac{\sigma_{ij}}{r_{ij}})^{q_{ij}} \right]
+                    \exp \left( \frac{\sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right) \\
+  \phi_3(r_{ij},r_{ik},\theta_{ijk}) & = f^{\textrm{3b}}\left(\theta_{ijk}\right)
+                    \exp \left( \frac{\gamma_{ij} \sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right)
+                    \exp \left( \frac{\gamma_{ik} \sigma_{ik}}{r_{ik} - a_{ik} \sigma_{ik}} \right)
+
+where :math:`\phi_2` is a two-body term and :math:`\phi_3` is a
+three-body term.  The summations in the formula are over all neighbors J
+and K of atom I within a cutoff distance :math:`a \sigma`.  In contrast
+to the original *sw* style, *sw/angle/table* allows for a flexible
+three-body term :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)` which
+is read in as a tabulated interaction. It can be parameterized with the
+csg_fmatch app of VOTCA as available at:
+https://gitlab.mpcdf.mpg.de/votca/votca.
+
+Only a single pair_coeff command is used with the *sw/angle/table* style
+which specifies a modified Stillinger-Weber potential file with
+parameters for all needed elements.  These are mapped to LAMMPS atom
+types by specifying N_el additional arguments after the ".sw" filename
+in the pair_coeff command, where N_el is the number of LAMMPS atom
+types:
+
+* ".sw" filename
+* N_el element names = mapping of SW elements to atom types
+
+See the :doc:`pair_coeff <pair_coeff>` page for alternate ways to
+specify the path for the potential file.
+
+As an example, imagine a file SiC.sw has Stillinger-Weber values for Si
+and C.  If your LAMMPS simulation has 4 atoms types and you want the
+first 3 to be Si, and the fourth to be C, you would use the following
+pair_coeff command:
+
+.. code-block:: LAMMPS
+
+   pair_coeff * * SiC.sw Si Si Si C
+
+The first 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 the Si
+element in the SW file.  The final C argument maps LAMMPS atom type 4 to
+the C element in the SW file.  If a mapping value is specified as NULL,
+the mapping is not performed.  This can be used when a *sw/angle/table*
+potential is used as part of the *hybrid* pair style.  The NULL values
+are placeholders for atom types that will be used with other potentials.
+
+The (modified) Stillinger-Weber files have a ".sw" suffix. Lines that
+are not blank or comments (starting with #) define parameters for a
+triplet of elements. The parameters in a single entry correspond to the
+two-body and three-body coefficients in the formula above. Here, also
+the suffix ".sw" is used though the original Stillinger-Weber file
+format is supplemented with four additional lines per parameter block to
+specify the tabulated three-body interaction. A single entry then
+contains:
+
+* element 1 (the center atom in a 3-body interaction)
+* element 2
+* element 3
+* :math:`\epsilon` (energy units)
+* :math:`\sigma` (distance units)
+* a
+* :math:`\lambda`
+* :math:`\gamma`
+* :math:`\cos\theta_0`
+* A
+* B
+* p
+* q
+* tol
+* filename
+* keyword
+* style
+* N
+
+The A, B, p, and q parameters are used only for two-body interactions.
+The :math:`\lambda` and :math:`\cos\theta_0` parameters, only used for
+three-body interactions in the original Stillinger-Weber style, are read
+in but ignored in this modified pair style. The :math:`\epsilon`
+parameter is only used for two-body interactions in this modified pair
+style and not for the three-body terms. The :math:`\sigma` and *a*
+parameters are used for both two-body and three-body
+interactions. :math:`\gamma` is used only in the three-body
+interactions, but is defined for pairs of atoms. The non-annotated
+parameters are unitless.
+
+LAMMPS introduces an additional performance-optimization parameter tol
+that is used for both two-body and three-body interactions.  In the
+Stillinger-Weber potential, the interaction energies become negligibly
+small at atomic separations substantially less than the theoretical
+cutoff distances.  LAMMPS therefore defines a virtual cutoff distance
+based on a user defined tolerance tol.  The use of the virtual cutoff
+distance in constructing atom neighbor lists can significantly reduce
+the neighbor list sizes and therefore the computational cost.  LAMMPS
+provides a *tol* value for each of the three-body entries so that they
+can be separately controlled. If tol = 0.0, then the standard
+Stillinger-Weber cutoff is used.
+
+The additional parameters *filename*, *keyword*, *style*, and *N* refer
+to the tabulated angular potential
+:math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)`.  The tabulated angular
+potential has to be of the format as used in the :doc:`angle_style table
+<angle_table>` command:
+
+An interpolation tables of length *N* is created. The interpolation is
+done in one of 2 *styles*: *linear* or *spline*.  For the *linear*
+style, the angle is used to find 2 surrounding table values from which
+an energy or its derivative is computed by linear interpolation. For the
+*spline* style, a cubic spline coefficients are computed and stored at
+each of the *N* values in the table.  The angle is used to find the
+appropriate set of coefficients which are used to evaluate a cubic
+polynomial which computes the energy or derivative.
+
+The *filename* specifies the file containing the tabulated energy and
+derivative values of :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)`.
+The *keyword* then specifies a section of the file.  The format of this
+file is as follows (without the parenthesized comments):
+
+.. parsed-literal::
+
+   # Angle potential for harmonic (one or more comment or blank lines)
+
+   HAM                           (keyword is the first text on line)
+   N 181 FP 0 0 EQ 90.0          (N, FP, EQ parameters)
+                                 (blank line)
+   1 0.0 200.5 2.5               (index, angle, energy, derivative)
+   2 1.0 198.0 2.5
+   ...
+   181 180.0 0.0 0.0
+
+A section begins with a non-blank line whose first character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections.  The first line begins with a keyword which identifies
+the section. The next line lists (in any order) one or more parameters
+for the table.  Each parameter is a keyword followed by one or more
+numeric values.
+
+The parameter "N" is required and its value is the number of table
+entries that follow.  Note that this may be different than the *N*
+specified in the Stillinger-Weber potential file. Let Nsw = *N* in the
+".sw" file, and Nfile = "N" in the tabulated angular file.  What LAMMPS
+does is a preliminary interpolation by creating splines using the Nfile
+tabulated values as nodal points.  It uses these to interpolate as
+needed to generate energy and derivative values at Ntable different
+points.  The resulting tables of length Nsw are then used as described
+above, when computing energy and force for individual angles and their
+atoms.  This means that if you want the interpolation tables of length
+Nsw to match exactly what is in the tabulated file (with effectively no
+preliminary interpolation), you should set Nsw = Nfile.
+
+The "FP" parameter is optional.  If used, it is followed by two values
+fplo and fphi, which are the second derivatives at the innermost and
+outermost angle settings.  These values are needed by the spline
+construction routines.  If not specified by the "FP" parameter, they are
+estimated (less accurately) by the first two and last two derivative
+values in the table.
+
+The "EQ" parameter is also optional.  If used, it is followed by a the
+equilibrium angle value, which is used, for example, by the :doc:`fix
+shake <fix_shake>` command. If not used, the equilibrium angle is set to
+180.0.
+
+Following a blank line, the next N lines of the angular table file list
+the tabulated values.  On each line, the first value is the index from 1
+to N, the second value is the angle value (in degrees), the third value
+is the energy (in energy units), and the fourth is -dE/d(theta) (also in
+energy units).  The third term is the energy of the 3-atom configuration
+for the specified angle.  The last term is the derivative of the energy
+with respect to the angle (in degrees, not radians).  Thus the units of
+the last term are still energy, not force.  The angle values must
+increase from one line to the next.  The angle values must also begin
+with 0.0 and end with 180.0, i.e. span the full range of possible
+angles.
+
+Note that one angular potential file can contain many sections, each
+with a tabulated potential.  LAMMPS reads the file section by section
+until it finds one that matches the specified *keyword* of appropriate
+section of the ".sw" file.
+
+The Stillinger-Weber potential file must contain entries for all the
+elements listed in the pair_coeff command.  It can also contain entries
+for additional elements not being used in a particular simulation;
+LAMMPS ignores those entries.
+
+For a single-element simulation, only a single entry is required
+(e.g. SiSiSi).  For a two-element simulation, the file must contain 8
+entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
+specify SW parameters for all permutations of the two elements
+interacting in three-body configurations.  Thus for 3 elements, 27
+entries would be required, etc.
+
+As annotated above, the first element in the entry is the center atom in
+a three-body interaction.  Thus an entry for SiCC means a Si atom with 2
+C atoms as neighbors.  The parameter values used for the two-body
+interaction come from the entry where the second and third elements are
+the same.  Thus the two-body parameters for Si interacting with C, comes
+from the SiCC entry.  The three-body angular potential
+:math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)` can in principle be
+specific to the three elements of the configuration. However, the user
+must ensure that it makes physically sense.  Note also that the function
+:math:`\phi_3` contains two exponential screening factors with parameter
+values from the ij pair and ik pairs. So :math:`\phi_3` for a C atom
+bonded to a Si atom and a second C atom will depend on the three-body
+parameters for the CSiC entry, and also on the two-body parameters for
+the CCC and CSiSi entries. Since the order of the two neighbors is
+arbitrary, the three-body parameters and the tabulated angular potential
+for entries CSiC and CCSi should be the same.  Similarly, the two-body
+parameters for entries SiCC and CSiSi should also be the same.  The
+parameters used only for two-body interactions (A, B, p, and q) in
+entries whose second and third element are different (e.g. SiCSi) are
+not used for anything and can be set to 0.0 if desired.  This is also
+true for the parameters in :math:`\phi_3` that are taken from the ij and
+ik pairs (:math:`\sigma`, *a*, :math:`\gamma`)
+
+Additional input files and reference data can be found at:
+https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-tutorials/spce/3body_sw
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as described
+above from values in the potential file, but not for the tabulated
+angular potential file.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart
+files <restart>`, since it is stored in potential files.  Thus, you need
+to re-specify the pair_style and pair_coeff commands in an input script
+that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  It does not support the
+*inner*, *middle*, *outer* keywords.
+
+----------
+
+Restrictions
+""""""""""""
+
+This pair style is part of the MANYBODY package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style sw <pair_sw>`, :doc:`pair_style threebody/table <pair_threebody_table>`
+
+
+----------
+
+.. _Stillinger3:
+
+**(Stillinger)** Stillinger and Weber, Phys Rev B, 31, 5262 (1985).
+
+.. _Scherer1:
+
+**(Scherer1)** C. Scherer and D. Andrienko, Phys. Chem. Chem. Phys. 20, 22387-22394 (2018).
+

doc/src/pair_threebody_table.rst

@@ -0,0 +1,281 @@
+.. index:: pair_style threebody/table
+
+pair_style threebody/table command
+==================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style style
+
+* style = *threebody/table*
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style threebody/table
+   pair_coeff * * spce2.3b type1 type2
+
+   pair_style hybrid/overlay table linear 1200 threebody/table
+   pair_coeff      1 1 table table_CG_CG.txt VOTCA
+   pair_coeff      * * threebody/table spce.3b type
+
+Used in example input scripts:
+
+.. parsed-literal::
+
+   examples/PACKAGES/manybody_table/in.spce
+   examples/PACKAGES/manybody_table/in.spce2
+
+Description
+"""""""""""
+
+The *threebody/table* style is a pair style for generic tabulated
+three-body interactions.  It has been developed for (coarse-grained)
+simulations (of water) with Kernel-based machine learning (ML)
+potentials (:ref:`Scherer2 <Scherer2>`).  As for many other MANYBODY
+package pair styles the energy of a system is computed as a sum over
+three-body terms:
+
+.. math::
+
+   E =  \sum_i \sum_{j \neq i} \sum_{k > j} \phi_3 (r_{ij}, r_{ik}, \theta_{ijk})
+
+The summations in the formula are over all neighbors J and K of atom I
+within a cutoff distance :math:`cut`.  In contrast to the
+Stillinger-Weber potential, all forces are not calculated analytically,
+but read in from a three-body force/energy table which can be generated
+with the csg_ml app of VOTCA as available at:
+https://gitlab.mpcdf.mpg.de/votca/votca.
+
+Only a single pair_coeff command is used with the *threebody/table*
+style which specifies a threebody potential (".3b") file with parameters
+for all needed elements. These are then mapped to LAMMPS atom types by
+specifying N_el additional arguments after the ".3b" filename in the
+pair_coeff command, where N_el is the number of LAMMPS atom types:
+
+* ".3b" filename
+* N_el element names = mapping of threebody elements to atom types
+
+See the :doc:`pair_coeff <pair_coeff>` page for alternate ways to
+specify the path for the potential file.
+
+As an example, imagine a file SiC.3b has three-body values for Si and C.
+If your LAMMPS simulation has 4 atoms types and you want the first 3 to
+be Si, and the fourth to be C, you would use the following pair_coeff
+command:
+
+.. code-block:: LAMMPS
+
+   pair_coeff * * SiC.3b Si Si Si C
+
+The first 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 the Si
+element in the ".3b" file.  The final C argument maps LAMMPS atom type 4
+to the C element in the threebody file. If a mapping value is specified
+as NULL, the mapping is not performed. This can be used when a
+*threebody/table* potential is used as part of the *hybrid* pair style.
+The NULL values are placeholders for atom types that will be used with
+other potentials.
+
+The three-body files have a ".3b" suffix. Lines that are not blank or
+comments (starting with #) define parameters for a triplet of
+elements. The parameters in a single entry specify to the (three-body)
+cutoff distance and the tabulated three-body interaction. A single entry
+then contains:
+
+* element 1 (the center atom in a 3-body interaction)
+* element 2
+* element 3
+* cut (distance units)
+* filename
+* keyword
+* style
+* N
+
+The parameter :math:`cut` is the (three-body) cutoff distance.  When set
+to 0, no interaction is calculated for this element triplet.  The
+parameters *filename*, *keyword*, *style*, and *N* refer to the
+tabulated three-body potential.
+
+The tabulation is done on a three-dimensional grid of the two distances
+:math:`r_{ij}` and :math:`r_{ik}` as well as the angle
+:math:`\theta_{ijk}` which is constructed in the following way. There
+are two different cases.  If element 2 and element 3 are of the same
+type (e.g. SiCC), the distance :math:`r_{ij}` is varied in "N" steps
+from rmin to rmax and the distance :math:`r_{ik}` is varied from
+:math:`r_{ij}` to rmax. This can be done, due to the symmetry of the
+triplet. If element 2 and element 3 are not of the same type
+(e.g. SiCSi), there is no additional symmetry and the distance
+:math:`r_{ik}` is also varied from rmin to rmax in "N" steps.  The angle
+:math:`\theta_{ijk}` is always varied in "2N" steps from (0.0 +
+180.0/(4N)) to (180.0 - 180.0/(4N)). Therefore, the total number of
+table entries is "M = N * N * (N+1)" for the symmetric (element 2 and
+element 3 are of the same type) and "M = 2 * N * N * N" for the general
+case (element 2 and element 3 are not of the same type).
+
+The forces on all three particles I, J, and K of a triplet of this type
+of three-body interaction potential (:math:`\phi_3 (r_{ij}, r_{ik},
+\theta_{ijk})`) lie within the plane defined by the three inter-particle
+distance vectors :math:`{\mathbf r}_{ij}`, :math:`{\mathbf r}_{ik}`, and
+:math:`{\mathbf r}_{jk}`.  This property is used to project the forces
+onto the inter-particle distance vectors as follows
+
+.. math::
+
+   \begin{pmatrix}
+      {\mathbf f}_{i} \\
+      {\mathbf f}_{j} \\
+      {\mathbf f}_{k} \\
+   \end{pmatrix} =
+   \begin{pmatrix}
+      f_{i1} & f_{i2} & 0 \\
+      f_{j1} & 0 & f_{j2} \\
+      0 & f_{k1} & f_{k2} \\
+   \end{pmatrix}
+   \begin{pmatrix}
+      {\mathbf r}_{ij} \\
+      {\mathbf r}_{ik} \\
+      {\mathbf r}_{jk} \\
+   \end{pmatrix}
+
+and then tabulate the 6 force constants :math:`f_{i1}`, :math:`f_{i2}`,
+:math:`f_{j1}`, :math:`f_{j2}`, :math:`f_{k1}`, and :math:`f_{k2}`, as
+well as the energy of a triplet e.  Due to symmetry reasons, the
+following relations hold: :math:`f_{i1}=-f_{j1}`,
+:math:`f_{i2}=-f_{k1}`, and :math:`f_{j2}=-f_{k2}`. As in this pair
+style the forces are read in directly, a correct MD simulation is also
+performed in the case that the triplet energies are set to e=0.
+
+The *filename* specifies the file containing the tabulated energy and
+derivative values of :math:`\phi_3 (r_{ij}, r_{ik}, \theta_{ijk})`.  The
+*keyword* then specifies a section of the file. The format of this file
+is as follows (without the parenthesized comments):
+
+.. parsed-literal::
+
+   # Tabulated three-body potential for spce water (one or more comment or blank lines)
+
+   ENTRY1                                                                      (keyword is the first text on line)
+   N 12 rmin 2.55 rmax 3.65                                                    (N, rmin, rmax parameters)
+                                                                               (blank line)
+   1 2.55 2.55 3.75 -867.212 -611.273 867.212 21386.8 611.273 -21386.8  0.0    (index, r_ij, r_ik, theta, f_i1, f_i2, f_j1, f_j2, f_k1, f_k2, e)
+   2 2.55 2.55 11.25 -621.539 -411.189 621.539 5035.95 411.189 -5035.95  0.0
+   ...
+   1872 3.65 3.65 176.25 -0.00215132 -0.00412886 0.00215137 0.00111754 0.00412895 -0.00111757  0.0
+
+A section begins with a non-blank line whose first character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections.  The first line begins with a keyword which identifies
+the section. The next line lists (in any order) one or more parameters
+for the table.  Each parameter is a keyword followed by one or more
+numeric values.
+
+The parameter "N" is required. It should be the same than the parameter
+"N" of the ".3b" file, otherwise its value is overwritten. "N"
+determines the number of table entries "M" that follow: "M = N * N *
+(N+1)" (symmetric triplet, e.g. SiCC) or "M = 2 * N * N * N" (asymmetric
+triplet, e.g. SiCSi). Therefore "M = 12 * 12 * 13 = 1872" in the above
+symmetric example. The parameters "rmin" and "rmax" are also required
+and determine the minimum and maximum of the inter-particle distances
+:math:`r_{ij}` and :math:`r_{ik}`.
+
+Following a blank line, the next M lines of the angular table file list
+the tabulated values.  On each line, the first value is the index from 1
+to M, the second value is the distance :math:`r_{ij}`, the third value
+is the distance :math:`r_{ik}`, the fourth value is the angle
+:math:`\theta_{ijk})`, the next six values are the force constants
+:math:`f_{i1}`, :math:`f_{i2}`, :math:`f_{j1}`, :math:`f_{j2}`,
+:math:`f_{k1}`, and :math:`f_{k2}`, and the last value is the energy e.
+
+Note that one three-body potential file can contain many sections, each
+with a tabulated potential. LAMMPS reads the file section by section
+until it finds one that matches the specified *keyword* of appropriate
+section of the ".3b" file.
+
+At the moment, only the *style* *linear* is allowed and
+implemented. After reading in the force table, it is internally stored
+in LAMMPS as a lookup table. For each triplet configuration occurring in
+the simulation within the cutoff distance, the next nearest tabulated
+triplet configuration is looked up. No interpolation is done.  This
+allows for a very efficient force calculation with the stored force
+constants and energies. Due to the know table structure, the lookup can
+be done efficiently. It has been tested (:ref:`Scherer2 <Scherer2>`)
+that with a reasonably small bin size, the accuracy and speed is
+comparable to that of a Stillinger-Weber potential with tabulated
+three-body interactions (:doc:`pair_style sw/angle/table
+<pair_sw_angle_table>`) while the table format of this pair style allows
+for more flexible three-body interactions.
+
+As for the Stillinger-Weber potential, the three-body potential file
+must contain entries for all the elements listed in the pair_coeff
+command.  It can also contain entries for additional elements not being
+used in a particular simulation; LAMMPS ignores those entries.
+
+For a single-element simulation, only a single entry is required
+(e.g. SiSiSi).  For a two-element simulation, the file must contain 8
+entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
+specify threebody parameters for all permutations of the two elements
+interacting in three-body configurations.  Thus for 3 elements, 27
+entries would be required, etc.
+
+As annotated above, the first element in the entry is the center atom in
+a three-body interaction. Thus an entry for SiCC means a Si atom with 2
+C atoms as neighbors. The tabulated three-body forces can in principle
+be specific to the three elements of the configuration.  However, the
+user must ensure that it makes physically sense.  E.g., the tabulated
+three-body forces for the entries CSiC and CCSi should be the same
+exchanging :math:`r_{ij}` with r_{ik}, :math:`f_{j1}` with
+:math:`f_{k1}`, and :math:`f_{j2}` with :math:`f_{k2}`.
+
+Additional input files and reference data can be found at:
+https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-tutorials/ml
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+As all interactions are tabulated, no mixing is performed.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart
+files <restart>`, since it is stored in potential files.  Thus, you need
+to re-specify the pair_style and pair_coeff commands in an input script
+that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  It does not support the
+*inner*, *middle*, *outer* keywords.
+
+----------
+
+Restrictions
+""""""""""""
+
+This pair style is part of the MANYBODY package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
+
+This pair style requires the :doc:`newton <newton>` setting to be "on"
+for pair interactions.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_coeff <pair_coeff>`, :doc:`pair sw/angle/table <pair_sw_angle_table>`
+
+
+----------
+
+.. _Scherer2:
+
+**(Scherer2)** C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, J. Chem. Theor. Comp. 16, 3194-3204 (2020).
+

doc/src/print.rst

@@ -46,6 +46,20 @@ lines of output, the string can be enclosed in triple quotes, as in
 the last example above.  If the text string contains variables, they
 will be evaluated and their current values printed.
 
+.. note::
+
+   As discussed on the :doc:`Commands parse <Commands_parse>` doc
+   page, the text string can use "immediate" variables, specified as
+   $(formula) with parenthesis, where the numeric formula has the same
+   syntax as equal-style variables described on the :doc:`variable
+   <variable>` doc page.  This is a convenient way to evaluate a
+   formula immediately without using the variable command to define a
+   named variable and then use that variable in the text string.  The
+   formula can include a trailing colon and format string which
+   determines the precision with which the numeric value is output.
+   This is also explained on the :doc:`Commands parse
+   <Commands_parse>` doc page.
+
 If the *file* or *append* keyword is used, a filename is specified to
 which the output will be written.  If *file* is used, then the
 filename is overwritten if it already exists.  If *append* is used,

doc/src/read_data.rst

@@ -56,7 +56,7 @@ Examples
    read_data ../run7/data.polymer.gz
    read_data data.protein fix mycmap crossterm CMAP
    read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
-   read_data data.water add merge 1 group solvent
+   read_data data.water add merge group solvent
 
 Description
 """""""""""
@@ -622,6 +622,8 @@ of analysis.
      - atom-ID molecule-ID atom-type x y z
    * - charge
      - atom-ID atom-type q x y z
+   * - dielectric
+     - atom-ID atom-type q x y z normx normy normz area ed em epsilon curvature
    * - dipole
      - atom-ID atom-type q x y z mux muy muz
    * - dpd

doc/src/read_restart.rst

@@ -11,7 +11,6 @@ Syntax
    read_restart file flag
 
 * file = name of binary restart file to read in
-* flag = remap (optional)
 
 Examples
 """"""""
@@ -19,44 +18,40 @@ Examples
 .. code-block:: LAMMPS
 
    read_restart save.10000
-   read_restart save.10000 remap
    read_restart restart.*
    read_restart restart.*.mpiio
-   read_restart poly.*.% remap
 
 Description
 """""""""""
 
 Read in a previously saved system configuration from a restart file.
 This allows continuation of a previous run.  Details about what
-information is stored (and not stored) in a restart file is given
-below.  Basically this operation will re-create the simulation box
-with all its atoms and their attributes as well as some related global
-settings, at the point in time it was written to the restart file by a
-previous simulation.  The simulation box will be partitioned into a
-regular 3d grid of rectangular bricks, one per processor, based on the
-number of processors in the current simulation and the settings of the
+information is stored (and not stored) in a restart file is given below.
+Basically this operation will re-create the simulation box with all its
+atoms and their attributes as well as some related global settings, at
+the point in time it was written to the restart file by a previous
+simulation.  The simulation box will be partitioned into a regular 3d
+grid of rectangular bricks, one per processor, based on the number of
+processors in the current simulation and the settings of the
 :doc:`processors <processors>` command.  The partitioning can later be
-changed by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
-
-.. note::
-
-   Normally, restart files are written by the
-   :doc:`restart <restart>` or :doc:`write_restart <write_restart>` commands
-   so that all atoms in the restart file are inside the simulation box.
-   If this is not the case, the read_restart command will print an error
-   that atoms were "lost" when the file is read.  This error should be
-   reported to the LAMMPS developers so the invalid writing of the
-   restart file can be fixed.  If you still wish to use the restart file,
-   the optional *remap* flag can be appended to the read_restart command.
-   This should avoid the error, by explicitly remapping each atom back
-   into the simulation box, updating image flags for the atom
-   appropriately.
+changed by the :doc:`balance <balance>` or :doc:`fix balance
+<fix_balance>` commands.
 
 Restart files are saved in binary format to enable exact restarts,
 meaning that the trajectories of a restarted run will precisely match
 those produced by the original run had it continued on.
 
+The binary restart file format was not designed with backward, forward,
+or cross-platform compatibility in mind, so the files are only expected
+to be read correctly by the same LAMMPS executable on the same platform.
+Changes to the architecture, compilation settings, or LAMMPS version can
+render a restart file unreadable or it may read the data incorrectly.
+If you want a more portable format, you can use the data file format as
+created by the :doc:`write_data <write_data>` command.  Binary restart
+files can also be converted into a data file from the command line by
+the LAMMPS executable that wrote them using the :ref:`-restart2data
+<restart2data>` command line flag.
+
 Several things can prevent exact restarts due to round-off effects, in
 which case the trajectories in the 2 runs will slowly diverge.  These
 include running on a different number of processors or changing
@@ -65,7 +60,8 @@ certain settings such as those set by the :doc:`newton <newton>` or
 these cases.
 
 Certain fixes will not restart exactly, though they should provide
-statistically similar results.  These include :doc:`fix shake <fix_shake>` and :doc:`fix langevin <fix_langevin>`.
+statistically similar results.  These include :doc:`fix shake
+<fix_shake>` and :doc:`fix langevin <fix_langevin>`.
 
 Certain pair styles will not restart exactly, though they should
 provide statistically similar results.  This is because the forces
@@ -81,18 +77,19 @@ produced the restart file, it could be a LAMMPS bug, so consider
 :doc:`reporting it <Errors_bugs>` if you think the behavior is a bug.
 
 Because restart files are binary, they may not be portable to other
-machines.  In this case, you can use the :doc:`-restart command-line switch <Run_options>` to convert a restart file to a data file.
+machines.  In this case, you can use the :doc:`-restart command-line
+switch <Run_options>` to convert a restart file to a data file.
 
-Similar to how restart files are written (see the
-:doc:`write_restart <write_restart>` and :doc:`restart <restart>`
-commands), the restart filename can contain two wild-card characters.
-If a "\*" appears in the filename, the directory is searched for all
-filenames that match the pattern where "\*" is replaced with a timestep
-value.  The file with the largest timestep value is read in.  Thus,
-this effectively means, read the latest restart file.  It's useful if
-you want your script to continue a run from where it left off.  See
-the :doc:`run <run>` command and its "upto" option for how to specify
-the run command so it does not need to be changed either.
+Similar to how restart files are written (see the :doc:`write_restart
+<write_restart>` and :doc:`restart <restart>` commands), the restart
+filename can contain two wild-card characters.  If a "\*" appears in the
+filename, the directory is searched for all filenames that match the
+pattern where "\*" is replaced with a timestep value.  The file with the
+largest timestep value is read in.  Thus, this effectively means, read
+the latest restart file.  It's useful if you want your script to
+continue a run from where it left off.  See the :doc:`run <run>` command
+and its "upto" option for how to specify the run command so it does not
+need to be changed either.
 
 If a "%" character appears in the restart filename, LAMMPS expects a
 set of multiple files to exist.  The :doc:`restart <restart>` and
@@ -222,17 +219,17 @@ its calculations in a consistent manner.
 
 .. note::
 
-   There are a handful of commands which can be used before or
-   between runs which may require a system initialization.  Examples
-   include the "balance", "displace_atoms", "delete_atoms", "set" (some
-   options), and "velocity" (some options) commands.  This is because
-   they can migrate atoms to new processors.  Thus they will also discard
-   unused "state" information from fixes.  You will know the discard has
+   There are a handful of commands which can be used before or between
+   runs which may require a system initialization.  Examples include the
+   "balance", "displace_atoms", "delete_atoms", "set" (some options),
+   and "velocity" (some options) commands.  This is because they can
+   migrate atoms to new processors.  Thus they will also discard unused
+   "state" information from fixes.  You will know the discard has
    occurred because a list of discarded fixes will be printed to the
    screen and log file, as explained above.  This means that if you wish
    to retain that info in a restarted run, you must re-specify the
-   relevant fixes and computes (which create fixes) before those commands
-   are used.
+   relevant fixes and computes (which create fixes) before those
+   commands are used.
 
 Some pair styles, like the :doc:`granular pair styles <pair_gran>`, also
 use a fix to store "state" information that persists from timestep to
@@ -245,18 +242,19 @@ LAMMPS allows bond interactions (angle, etc) to be turned off or
 deleted in various ways, which can affect how their info is stored in
 a restart file.
 
-If bonds (angles, etc) have been turned off by the :doc:`fix shake <fix_shake>` or :doc:`delete_bonds <delete_bonds>` command,
-their info will be written to a restart file as if they are turned on.
-This means they will need to be turned off again in a new run after
-the restart file is read.
+If bonds (angles, etc) have been turned off by the :doc:`fix shake
+<fix_shake>` or :doc:`delete_bonds <delete_bonds>` command, their info
+will be written to a restart file as if they are turned on.  This means
+they will need to be turned off again in a new run after the restart
+file is read.
 
 Bonds that are broken (e.g. by a bond-breaking potential) are written
 to the restart file as broken bonds with a type of 0.  Thus these
 bonds will still be broken when the restart file is read.
 
-Bonds that have been broken by the :doc:`fix bond/break <fix_bond_break>` command have disappeared from the
-system.  No information about these bonds is written to the restart
-file.
+Bonds that have been broken by the :doc:`fix bond/break
+<fix_bond_break>` command have disappeared from the system.  No
+information about these bonds is written to the restart file.
 
 ----------
 

doc/src/special_bonds.rst

@@ -88,7 +88,7 @@ The Coulomb factors are applied to any Coulomb (charge interaction)
 term that the potential calculates.  The LJ factors are applied to the
 remaining terms that the potential calculates, whether they represent
 LJ interactions or not.  The weighting factors are a scaling
-pre-factor on the energy and force between the pair of atoms.  A value
+prefactor on the energy and force between the pair of atoms.  A value
 of 1.0 means include the full interaction; a value of 0.0 means
 exclude it completely.
 

doc/src/variable.rst

@@ -11,7 +11,7 @@ Syntax
    variable name style args ...
 
 * name = name of variable to define
-* style = *delete* or *index* or *loop* or *world* or *universe* or *uloop* or *string* or *format* or *getenv* or *file* or *atomfile* or *python* or *internal* or *equal* or *vector* or *atom*
+* style = *delete* or *index* or *loop* or *world* or *universe* or *uloop* or *string* or *format* or *getenv* or *file* or *atomfile* or *python* or *timer* or *internal* or *equal* or *vector* or *atom*
 
   .. parsed-literal::
 
@@ -42,6 +42,7 @@ Syntax
        *file* arg = filename
        *atomfile* arg = filename
        *python* arg = function
+       *timer* arg = no arguments
        *internal* arg = numeric value
        *equal* or *vector* or *atom* args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
          numbers = 0.0, 100, -5.4, 2.8e-4, etc
@@ -96,6 +97,13 @@ Examples
    variable str format x %.6g
    variable x delete
 
+.. code-block:: LAMMPS
+
+   variable start timer
+   other commands
+   variable stop timer
+   print "Elapsed time: $(v_stop-v_start:%.6f)"
+
 Description
 """""""""""
 
@@ -108,32 +116,38 @@ part of a new input command.  For variable styles that store multiple
 strings, the :doc:`next <next>` command can be used to increment which
 string is assigned to the variable.  Variables of style *equal* store
 a formula which when evaluated produces a single numeric value which
-can be output either directly (see the :doc:`print <print>`, :doc:`fix print <fix_print>`, and :doc:`run every <run>` commands) or as part
-of thermodynamic output (see the :doc:`thermo_style <thermo_style>`
-command), or used as input to an averaging fix (see the :doc:`fix ave/time <fix_ave_time>` command).  Variables of style *vector*
-store a formula which produces a vector of such values which can be
-used as input to various averaging fixes, or elements of which can be
-part of thermodynamic output.  Variables of style *atom* store a
-formula which when evaluated produces one numeric value per atom which
-can be output to a dump file (see the :doc:`dump custom <dump>` command)
-or used as input to an averaging fix (see the :doc:`fix ave/chunk <fix_ave_chunk>` and :doc:`fix ave/atom <fix_ave_atom>`
-commands).  Variables of style *atomfile* can be used anywhere in an
-input script that atom-style variables are used; they get their
-per-atom values from a file rather than from a formula.  Variables of
-style *python* can be hooked to Python functions using code you
-provide, so that the variable gets its value from the evaluation of
-the Python code.  Variables of style *internal* are used by a few
-commands which set their value directly.
+can be output either directly (see the :doc:`print <print>`, :doc:`fix
+print <fix_print>`, and :doc:`run every <run>` commands) or as part of
+thermodynamic output (see the :doc:`thermo_style <thermo_style>`
+command), or used as input to an averaging fix (see the :doc:`fix
+ave/time <fix_ave_time>` command).  Variables of style *vector* store
+a formula which produces a vector of such values which can be used as
+input to various averaging fixes, or elements of which can be part of
+thermodynamic output.  Variables of style *atom* store a formula which
+when evaluated produces one numeric value per atom which can be output
+to a dump file (see the :doc:`dump custom <dump>` command) or used as
+input to an averaging fix (see the :doc:`fix ave/chunk
+<fix_ave_chunk>` and :doc:`fix ave/atom <fix_ave_atom>` commands).
+Variables of style *atomfile* can be used anywhere in an input script
+that atom-style variables are used; they get their per-atom values
+from a file rather than from a formula.  Variables of style *python*
+can be hooked to Python functions using code you provide, so that the
+variable gets its value from the evaluation of the Python code.
+Variables of style *internal* are used by a few commands which set
+their value directly.
 
 .. note::
 
    As discussed on the :doc:`Commands parse <Commands_parse>` doc
    page, an input script can use "immediate" variables, specified as
-   $(formula) with parenthesis, where the formula has the same syntax as
-   equal-style variables described on this page.  This is a convenient
-   way to evaluate a formula immediately without using the variable
-   command to define a named variable and then evaluate that
-   variable. See below for a more detailed discussion of this feature.
+   $(formula) with parenthesis, where the numeric formula has the same
+   syntax as equal-style variables described on this page.  This is a
+   convenient way to evaluate a formula immediately without using the
+   variable command to define a named variable and then evaluate that
+   variable.  The formula can include a trailing colon and format
+   string which determines the precision with which the numeric value
+   is generated.  This is also explained on the :doc:`Commands parse
+   <Commands_parse>` doc page.
 
 In the discussion that follows, the "name" of the variable is the
 arbitrary string that is the first argument in the variable command.
@@ -160,22 +174,19 @@ simulation.
 
 Variables of style *equal* and *vector* and *atom* can be used as
 inputs to various other commands which evaluate their formulas as
-needed, e.g. at different timesteps during a :doc:`run <run>`.
+needed, e.g. at different timesteps during a :doc:`run <run>`.  In
+this context, variables of style *timer* or *internal* or *python* can
+be used in place of an equal-style variable, with the following two
+caveats.
 
-Variables of style *internal* can be used in place of an equal-style
-variable, except by commands that set the value stored by the
-internal-style variable.  Thus any command that states it can use an
-equal-style variable as an argument, can also use an internal-style
-variable.  This means that when the command evaluates the variable, it
-will use the value set (internally) by another command.
-
-Variables of style *python* can be used in place of an equal-style
-variable so long as the associated Python function, as defined by the
-:doc:`python <python>` command, returns a numeric value.  Thus any
-command that states it can use an equal-style variable as an argument,
-can also use such a python-style variable.  This means that when the
-LAMMPS command evaluates the variable, the Python function will be
-executed.
+First, internal-style variables can be used except by commands that
+set the value stored by the internal variable.  When the LAMMPS
+command evaluates the internal-style variable, it will use the value
+set (internally) by another command.  Second, python-style variables
+can be used so long as the associated Python function, as defined by
+the :doc:`python <python>` command, returns a numeric value.  When the
+LAMMPS command evaluates the python-style variable, the Python
+function will be executed.
 
 .. note::
 
@@ -271,14 +282,15 @@ N1 <= N2 and N2 >= 0 is required.
 
 For the *world* style, one or more strings are specified.  There must
 be one string for each processor partition or "world".  LAMMPS can be
-run with multiple partitions via the :doc:`-partition command-line switch <Run_options>`.  This variable command assigns one string to
+run with multiple partitions via the :doc:`-partition command-line
+switch <Run_options>`.  This variable command assigns one string to
 each world.  All processors in the world are assigned the same string.
 The next command cannot be used with *equal* style variables, since
 there is only one value per world.  This style of variable is useful
 when you wish to run different simulations on different partitions, or
-when performing a parallel tempering simulation (see the
-:doc:`temper <temper>` command), to assign different temperatures to
-different partitions.
+when performing a parallel tempering simulation (see the :doc:`temper
+<temper>` command), to assign different temperatures to different
+partitions.
 
 For the *universe* style, one or more strings are specified.  There
 must be at least as many strings as there are processor partitions or
@@ -313,11 +325,12 @@ appropriate for formatting a double-precision floating-point value.
 The default format is "%.15g".  This variable style allows an
 equal-style variable to be formatted precisely when it is evaluated.
 
-If you simply wish to print a variable value with desired precision to
-the screen or logfile via the :doc:`print <print>` or :doc:`fix print <fix_print>` commands, you can also do this by specifying an
-"immediate" variable with a trailing colon and format string, as part
-of the string argument of those commands.  This is explained on the
-:doc:`Commands parse <Commands_parse>` doc page.
+Note that if you simply wish to print a variable value with desired
+precision to the screen or logfile via the :doc:`print <print>` or
+:doc:`fix print <fix_print>` commands, you can also do this by
+specifying an "immediate" variable with a trailing colon and format
+string, as part of the string argument of those commands.  This is
+explained on the :doc:`Commands parse <Commands_parse>` doc page.
 
 For the *getenv* style, a single string is assigned to the variable
 which should be the name of an environment variable.  When the
@@ -412,14 +425,25 @@ python-style variable can be used in place of an equal-style variable
 anywhere in an input script, e.g. as an argument to another command
 that allows for equal-style variables.
 
+For the *timer* style no additional argument is specified.  The value of
+the variable is set by querying the current elapsed wall time of the
+simulation.  This is done at the point in time when the variable is
+defined in the input script.  If a second timer-style variable is also
+defined, then a simple formula can be used to calculate the elapsed time
+between the two timers, as in the example at the top of this manual
+entry.  As mentioned above, timer-style variables can be redefined
+elsewhere in the input script, so the same pair of variables can be used
+in a loop or to time a series of operations.
+
 For the *internal* style a numeric value is provided.  This value will
 be assigned to the variable until a LAMMPS command sets it to a new
 value.  There are currently only two LAMMPS commands that require
 *internal* variables as inputs, because they reset them:
-:doc:`create_atoms <create_atoms>` and :doc:`fix controller <fix_controller>`.  As mentioned above, an
-internal-style variable can be used in place of an equal-style
-variable anywhere else in an input script, e.g. as an argument to
-another command that allows for equal-style variables.
+:doc:`create_atoms <create_atoms>` and :doc:`fix controller
+<fix_controller>`.  As mentioned above, an internal-style variable can
+be used in place of an equal-style variable anywhere else in an input
+script, e.g. as an argument to another command that allows for
+equal-style variables.
 
 ----------
 
@@ -823,15 +847,6 @@ Special Functions
 Special functions take specific kinds of arguments, meaning their
 arguments cannot be formulas themselves.
 
-The is_file(name) function is a test whether *name* is a (readable) file
-and returns 1 in this case, otherwise it returns 0.  For that *name*
-is taken as a literal string and must not have any blanks in it.
-
-The extract_setting(name) function allows to access some basic settings
-through calling the :cpp:func:`lammps_extract_setting` library function.
-For available keywords *name* and their meaning, please see the
-documentation of that function.
-
 The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions
 each take 1 argument which is of the form "c_ID" or "c_ID[N]" or
 "f_ID" or "f_ID[N]" or "v_name".  The first two are computes and the
@@ -910,6 +925,19 @@ invoked more times than there are lines or sets of lines in the file,
 the variable is deleted, similar to how the :doc:`next <next>` command
 operates.
 
+The is_file(name) function is a test whether *name* is a (readable) file
+and returns 1 in this case, otherwise it returns 0.  For that *name*
+is taken as a literal string and must not have any blanks in it.
+
+The extract_setting(name) function enables access to basic settings for
+the LAMMPS executable and the running simulation via calling the
+:cpp:func:`lammps_extract_setting` library function.  For example, the
+number of processors (MPI ranks) being used by the simulation or the MPI
+process ID (for this processor) can be queried, or the number of atom
+types, bond types and so on. For the full list of available keywords
+*name* and their meaning, see the documentation for extract_setting()
+via the link in this paragraph.
+
 ----------
 
 Feature Functions
@@ -1383,14 +1411,15 @@ commands:
 The first run is performed using one setting for the pairwise
 potential defined by the :doc:`pair_style <pair_style>` and
 :doc:`pair_coeff <pair_coeff>` commands.  The potential energy is
-evaluated on the final timestep and stored by the :doc:`compute pe <compute_pe>` compute (this is done by the
-:doc:`thermo_style <thermo_style>` command).  Then a pair coefficient is
-changed, altering the potential energy of the system.  When the
-potential energy is printed via the "e" variable, LAMMPS will use the
-potential energy value stored by the :doc:`compute pe <compute_pe>`
-compute, thinking it is current.  There are many other commands which
-could alter the state of the system between runs, causing a variable
-to evaluate incorrectly.
+evaluated on the final timestep and stored by the :doc:`compute pe
+<compute_pe>` compute (this is done by the :doc:`thermo_style
+<thermo_style>` command).  Then a pair coefficient is changed,
+altering the potential energy of the system.  When the potential
+energy is printed via the "e" variable, LAMMPS will use the potential
+energy value stored by the :doc:`compute pe <compute_pe>` compute,
+thinking it is current.  There are many other commands which could
+alter the state of the system between runs, causing a variable to
+evaluate incorrectly.
 
 The solution to this issue is the same as for case (2) above, namely
 perform a 0-timestep run before the variable is evaluated to insure

doc/utils/requirements.txt

@@ -6,4 +6,3 @@ breathe
 Pygments
 six
 pyyaml
-wheel

doc/utils/sphinx-config/false_positives.txt

@@ -94,6 +94,7 @@ amu
 Amzallag
 analytical
 Anders
+Andrienko
 Andzelm
 Ang
 anglegrad
@@ -119,6 +120,7 @@ Antonelli
 api
 Apoorva
 Appl
+apptainer
 Apu
 arallel
 arccos
@@ -239,6 +241,7 @@ benchmarking
 Bennet
 Berardi
 Beraun
+Bereau
 berendsen
 Berendsen
 berger
@@ -444,6 +447,7 @@ chris
 Christoph
 Chu
 chunkID
+chunksize
 Ciccotti
 Cieplak
 Cii
@@ -559,6 +563,7 @@ Crozier
 Cryst
 Crystallogr
 Csanyi
+csg
 csh
 cshrc
 CSiC
@@ -872,6 +877,7 @@ Eindhoven
 Eisenforschung
 Ejtehadi
 El
+el
 elaplong
 elastance
 Electroneg
@@ -1080,6 +1086,7 @@ fm
 fmackay
 fmag
 fmass
+fmatch
 fmm
 fmt
 fmtlib
@@ -1318,6 +1325,7 @@ hexatic
 hexorder
 Heyes
 HfO
+hftn
 hgrid
 hhmrr
 Hibbs
@@ -1326,6 +1334,7 @@ hiID
 Hijazi
 Hilger
 Hinestrosa
+hipFFT
 histo
 histogrammed
 histogramming
@@ -1561,6 +1570,7 @@ jpeglib
 jpg
 JPG
 jpl
+json
 Jth
 jtranch
 jtype
@@ -1695,6 +1705,7 @@ lamda
 lammps
 Lammps
 LAMMPS
+lammpsbin
 lammpsplot
 lammpsplugin
 Lamoureux
@@ -1951,6 +1962,7 @@ maxsize
 maxspecial
 maxSteps
 maxstrain
+maxtry
 maxwell
 Maxwellian
 maxX
@@ -2227,6 +2239,7 @@ Navier
 nb
 Nbin
 Nbins
+nbodies
 nbody
 Nbody
 nbond
@@ -2266,6 +2279,7 @@ nelem
 Nelement
 Nelements
 nelems
+nellipsoids
 nemd
 netapp
 netcdf
@@ -2355,7 +2369,11 @@ nopreliminary
 Nord
 norder
 Nordlund
+noremap
 normals
+normx
+normy
+normz
 Noskov
 noslip
 noticable
@@ -2399,6 +2417,7 @@ Nstep
 Nsteplast
 Nstop
 nsub
+Nsw
 Nswap
 nt
 Nt
@@ -2408,6 +2427,7 @@ nthreads
 ntimestep
 Ntptask
 Ntriples
+ntris
 Ntype
 ntypes
 Ntypes
@@ -2791,6 +2811,7 @@ quatk
 quatw
 queryargs
 Queteschiner
+quickmin
 qw
 qx
 qy
@@ -2951,6 +2972,7 @@ rnage
 rng
 rNEMD
 ro
+rocFFT
 Rochus
 Rockett
 rocksalt
@@ -3026,6 +3048,7 @@ scalexz
 scaleyz
 Scalfi
 Schaik
+Scheid
 Schilfgarde
 Schimansky
 Schiotz
@@ -3043,6 +3066,7 @@ screenshot
 screenshots
 Scripps
 Scripta
+sd
 sdk
 sdpd
 SDPD
@@ -3202,6 +3226,7 @@ statvolt
 stdin
 stdio
 stdlib
+stdout
 steelblue
 Stegailov
 Steinbach
@@ -3213,6 +3238,7 @@ Stesmans
 stiffnesses
 Stillinger
 stk
+stl
 stochastically
 stochasticity
 Stockmayer

examples/COUPLE/fortran2/LAMMPS-wrapper.cpp

@@ -12,8 +12,8 @@
 ------------------------------------------------------------------------- */
 
 /* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
-                          University of Tennessee, Knoxville (USA), 2012
+    Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
+                          University of Missouri (USA), 2012
 ------------------------------------------------------------------------- */
 
 /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
@@ -23,6 +23,7 @@
 
 #include <mpi.h>
 #include "LAMMPS-wrapper.h"
+#define LAMMPS_LIB_MPI 1
 #include <library.h>
 #include <lammps.h>
 #include <atom.h>
@@ -56,181 +57,40 @@ void lammps_error_all (void *ptr, const char *file, int line, const char *str)
 
 int lammps_extract_compute_vectorsize (void *ptr, char *id, int style)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
-   int icompute = lmp->modify->find_compute(id);
-   if ( icompute < 0 ) return 0;
-   class Compute *compute = lmp->modify->compute[icompute];
-
-   if ( style == 0 )
-   {
-      if ( !compute->vector_flag )
-         return 0;
-      else
-         return compute->size_vector;
-   }
-   else if ( style == 1 )
-   {
-      return lammps_get_natoms (ptr);
-   }
-   else if ( style == 2 )
-   {
-      if ( !compute->local_flag )
-         return 0;
-      else
-         return compute->size_local_rows;
-   }
-   else
-      return 0;
+   int *size;
+   size = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_VECTOR);
+   if (size) return *size;
+   return 0;
 }
 
 void lammps_extract_compute_arraysize (void *ptr, char *id, int style,
       int *nrows, int *ncols)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
-   int icompute = lmp->modify->find_compute(id);
-   if ( icompute < 0 )
-   {
-      *nrows = 0;
-      *ncols = 0;
-   }
-   class Compute *compute = lmp->modify->compute[icompute];
-
-   if ( style == 0 )
-   {
-      if ( !compute->array_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = compute->size_array_rows;
-         *ncols = compute->size_array_cols;
-      }
-   }
-   else if ( style == 1 )
-   {
-      if ( !compute->peratom_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = lammps_get_natoms (ptr);
-         *ncols = compute->size_peratom_cols;
-      }
-   }
-   else if ( style == 2 )
-   {
-      if ( !compute->local_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = compute->size_local_rows;
-         *ncols = compute->size_local_cols;
-      }
-   }
-   else
-   {
-      *nrows = 0;
-      *ncols = 0;
-   }
-
+   int *tmp;
+   tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_ROWS);
+   if (tmp) *nrows = *tmp;
+   tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_COLS);
+   if (tmp) *ncols = *tmp;
    return;
 }
 
 int lammps_extract_fix_vectorsize (void *ptr, char *id, int style)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
-   int ifix = lmp->modify->find_fix(id);
-   if ( ifix < 0 ) return 0;
-   class Fix *fix = lmp->modify->fix[ifix];
-
-   if ( style == 0 )
-   {
-      if ( !fix->vector_flag )
-         return 0;
-      else
-         return fix->size_vector;
-   }
-   else if ( style == 1 )
-   {
-      return lammps_get_natoms (ptr);
-   }
-   else if ( style == 2 )
-   {
-      if ( !fix->local_flag )
-         return 0;
-      else
-         return fix->size_local_rows;
-   }
-   else
-      return 0;
+   int *size;
+   size = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_VECTOR, 0, 0);
+   if (size) return *size;
+   return 0;
 }
 
 void lammps_extract_fix_arraysize (void *ptr, char *id, int style,
       int *nrows, int *ncols)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
-   int ifix = lmp->modify->find_fix(id);
-   if ( ifix < 0 )
-   {
-      *nrows = 0;
-      *ncols = 0;
-   }
-   class Fix *fix = lmp->modify->fix[ifix];
-
-   if ( style == 0 )
-   {
-      if ( !fix->array_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = fix->size_array_rows;
-         *ncols = fix->size_array_cols;
-      }
-   }
-   else if ( style == 1 )
-   {
-      if ( !fix->peratom_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = lammps_get_natoms (ptr);
-         *ncols = fix->size_peratom_cols;
-      }
-   }
-   else if ( style == 2 )
-   {
-      if ( !fix->local_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = fix->size_local_rows;
-         *ncols = fix->size_local_cols;
-      }
-   }
-   else
-   {
-      *nrows = 0;
-      *ncols = 0;
-   }
-
+   int *tmp;
+   tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_ROWS, 0, 0);
+   if (tmp) *nrows = *tmp;
+   tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_COLS, 0, 0);
+   if (tmp) *ncols = *tmp;
    return;
-
 }
 
 /* vim: set ts=3 sts=3 expandtab: */

examples/COUPLE/fortran2/LAMMPS-wrapper.h

@@ -12,8 +12,8 @@
 ------------------------------------------------------------------------- */
 
 /* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
-                          University of Tennessee, Knoxville (USA), 2012
+    Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
+                          University of Missouri (USA), 2012
 ------------------------------------------------------------------------- */
 
 /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

examples/COUPLE/fortran2/LAMMPS.F90

@@ -1292,7 +1292,7 @@ contains !! Wrapper functions local to this module {{{1
       Cname = string2Cstring (name)
       Ccount = size(data) / natoms
       if ( Ccount /= 1 .and. Ccount /= 3 ) &
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
+         call lammps_error_all (ptr, FLERR, 'lammps_scatter_atoms requires&
             & count to be either 1 or 3')
       Fdata = data
       Cdata = C_loc (Fdata(1))
@@ -1355,7 +1355,7 @@ contains !! Wrapper functions local to this module {{{1
       Cname = string2Cstring (name)
       Ccount = size(data) / ndata
       if ( Ccount /= 1 .and. Ccount /= 3 ) &
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
+         call lammps_error_all (ptr, FLERR, 'lammps_scatter_atoms requires&
             & count to be either 1 or 3')
       Fdata = data
       Cdata = C_loc (Fdata(1))

examples/COUPLE/fortran2/Makefile

@@ -14,7 +14,7 @@ CXXLIB = -lstdc++    # replace with your C++ runtime libs
 # Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively
 FFLAGS = -O2 -fPIC
 CXXFLAGS = -O2 -fPIC
-CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX -DLAMMPS_LIB_MPI
+CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX
 
 all : liblammps_fortran.a liblammps_fortran.so
 

examples/COUPLE/fortran2/README

@@ -11,9 +11,8 @@ This interface was created by Karl Hammond who you can contact with
 questions:
 
 Karl D. Hammond
-University of Tennessee, Knoxville
-karlh at ugcs.caltech.edu
-karlh at utk.edu
+University of Missouri
+hammondkd at missouri.edu
 
 -------------------------------------
 

examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp

@@ -12,8 +12,8 @@
 ------------------------------------------------------------------------- */
 
 /* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
-                          University of Tennessee, Knoxville (USA), 2012
+    Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
+                          University of Missouri (USA), 2012
 ------------------------------------------------------------------------- */
 
 /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
@@ -23,6 +23,7 @@
 
 #include <mpi.h>
 #include "LAMMPS-wrapper.h"
+#define LAMMPS_LIB_MPI 1
 #include <library.h>
 #include <lammps.h>
 #include <atom.h>
@@ -56,181 +57,40 @@ void lammps_error_all (void *ptr, const char *file, int line, const char *str)
 
 int lammps_extract_compute_vectorsize (void *ptr, char *id, int style)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
-   int icompute = lmp->modify->find_compute(id);
-   if ( icompute < 0 ) return 0;
-   class Compute *compute = lmp->modify->compute[icompute];
-
-   if ( style == 0 )
-   {
-      if ( !compute->vector_flag )
-         return 0;
-      else
-         return compute->size_vector;
-   }
-   else if ( style == 1 )
-   {
-      return lammps_get_natoms (ptr);
-   }
-   else if ( style == 2 )
-   {
-      if ( !compute->local_flag )
-         return 0;
-      else
-         return compute->size_local_rows;
-   }
-   else
-      return 0;
+   int *size;
+   size = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_VECTOR);
+   if (size) return *size;
+   return 0;
 }
 
 void lammps_extract_compute_arraysize (void *ptr, char *id, int style,
       int *nrows, int *ncols)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
-   int icompute = lmp->modify->find_compute(id);
-   if ( icompute < 0 )
-   {
-      *nrows = 0;
-      *ncols = 0;
-   }
-   class Compute *compute = lmp->modify->compute[icompute];
-
-   if ( style == 0 )
-   {
-      if ( !compute->array_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = compute->size_array_rows;
-         *ncols = compute->size_array_cols;
-      }
-   }
-   else if ( style == 1 )
-   {
-      if ( !compute->peratom_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = lammps_get_natoms (ptr);
-         *ncols = compute->size_peratom_cols;
-      }
-   }
-   else if ( style == 2 )
-   {
-      if ( !compute->local_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = compute->size_local_rows;
-         *ncols = compute->size_local_cols;
-      }
-   }
-   else
-   {
-      *nrows = 0;
-      *ncols = 0;
-   }
-
+   int *tmp;
+   tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_ROWS);
+   if (tmp) *nrows = *tmp;
+   tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_COLS);
+   if (tmp) *ncols = *tmp;
    return;
 }
 
 int lammps_extract_fix_vectorsize (void *ptr, char *id, int style)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
-   int ifix = lmp->modify->find_fix(id);
-   if ( ifix < 0 ) return 0;
-   class Fix *fix = lmp->modify->fix[ifix];
-
-   if ( style == 0 )
-   {
-      if ( !fix->vector_flag )
-         return 0;
-      else
-         return fix->size_vector;
-   }
-   else if ( style == 1 )
-   {
-      return lammps_get_natoms (ptr);
-   }
-   else if ( style == 2 )
-   {
-      if ( !fix->local_flag )
-         return 0;
-      else
-         return fix->size_local_rows;
-   }
-   else
-      return 0;
+   int *size;
+   size = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_VECTOR, 0, 0);
+   if (size) return *size;
+   return 0;
 }
 
 void lammps_extract_fix_arraysize (void *ptr, char *id, int style,
       int *nrows, int *ncols)
 {
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
-   int ifix = lmp->modify->find_fix(id);
-   if ( ifix < 0 )
-   {
-      *nrows = 0;
-      *ncols = 0;
-   }
-   class Fix *fix = lmp->modify->fix[ifix];
-
-   if ( style == 0 )
-   {
-      if ( !fix->array_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = fix->size_array_rows;
-         *ncols = fix->size_array_cols;
-      }
-   }
-   else if ( style == 1 )
-   {
-      if ( !fix->peratom_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = lammps_get_natoms (ptr);
-         *ncols = fix->size_peratom_cols;
-      }
-   }
-   else if ( style == 2 )
-   {
-      if ( !fix->local_flag )
-      {
-         *nrows = 0;
-         *ncols = 0;
-      }
-      else
-      {
-         *nrows = fix->size_local_rows;
-         *ncols = fix->size_local_cols;
-      }
-   }
-   else
-   {
-      *nrows = 0;
-      *ncols = 0;
-   }
-
+   int *tmp;
+   tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_ROWS, 0, 0);
+   if (tmp) *nrows = *tmp;
+   tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_COLS, 0, 0);
+   if (tmp) *ncols = *tmp;
    return;
-
 }
 
 /* vim: set ts=3 sts=3 expandtab: */

examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h

@@ -12,8 +12,8 @@
 ------------------------------------------------------------------------- */
 
 /* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
-                          University of Tennessee, Knoxville (USA), 2012
+    Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
+                          University of Missouri (USA), 2012
 ------------------------------------------------------------------------- */
 
 /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp

@@ -12,8 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
-                          University of Tennessee, Knoxville (USA), 2012
+    Contributing author:  Nir Goldman, LLNL <ngoldman@llnl.gov>, 2016
 ------------------------------------------------------------------------- */
 
 /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ------------------------------------------------------------------------
-    Contributing author:  Nir Goldman, ngoldman@llnl.gov, Oct. 19th, 2016
+    Contributing author:  Nir Goldman, LLNL <ngoldman@llnl.gov>, 2016
 ------------------------------------------------------------------------- */
 
 /* This is set of "wrapper" functions to assist LAMMPS.F90, which itself

examples/COUPLE/fortran_dftb/LAMMPS.F90

@@ -12,8 +12,8 @@
 !--------------------------------------------------------------------------
 
 !! ------------------------------------------------------------------------
-!   Contributing author:  Karl D. Hammond <karlh@ugcs.caltech.edu>
-!                         University of Tennessee, Knoxville (USA), 2012
+!   Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
+!                         University of Missouri (USA), 2012
 !--------------------------------------------------------------------------
 
 !! LAMMPS, a Fortran 2003 module containing an interface between Fortran

examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/compute_born.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-import sys
 import numpy as np
 
 def reduce_Born(Cf):

examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/compute_born.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-import sys
 import numpy as np
 
 def reduce_Born(Cf):

examples/ELASTIC_T/BORN_MATRIX/Silicon/README

@@ -0,0 +1,37 @@
+This directory shows how to use the `fix born` command
+to calculate the full matrix of elastic constants
+for cubic diamond at finite temperature
+running the Stillinger-Weber potential.
+
+The input script `in.elastic` can be run
+directly from LAMMPS, or via a Python wrapper
+script.
+
+to run directly from LAMMPS, use:
+
+mpirun -np 4 lmp.exe -in in.elastic
+
+This simulates an orthorhombic box with the cubic crystal axes
+aligned with x, y, and z.
+The default settings replicate the 1477~K benchmark of
+Kluge, Ray, and Rahman (1986) that is Ref.[15] in:
+Y. Zhen, C. Chu, Computer Physics Communications 183(2012) 261-265
+
+The script contains many adjustable parameters that can be used
+to generate different crystal structures, supercell sizes,
+and sampling rates.
+
+to run via the Python wrapper, use:
+
+mpirun -np 4 python elastic.py
+
+This will first run the orthorhombic supercell as before,
+follows by an equivalent simulation using a triclinic structure.
+The script shows how the standard triclinic primitive cell for cubic diamond
+can be rotated in to the LAMMPS upper triangular frame. The resultant
+elastic constant matrix does not exhibit the standard symmetries of cubic crystals.
+However, the matrix is then rotated back to the standard orientation
+to recover the cubic symmetry form of the elastic matrix,
+resulting in elastic constants that are the same for both
+simulations, modulo statistical uncertainty.
+

examples/ELASTIC_T/BORN_MATRIX/Silicon/elastic.py

@@ -0,0 +1,114 @@
+#!/usr/bin/env python -i
+# preceding line should have path for Python on your machine
+
+# elastic.py
+# Purpose: demonstrate elastic constant calculation for
+# two different crystal supercells, one with non-standard orientation
+#
+# Syntax:  elastic.py
+#          uses in.elastic as LAMMPS input script
+
+from __future__ import print_function
+from elastic_utils import *
+
+np.set_printoptions(precision = 3, suppress=True)
+
+# get MPI settings from LAMMPS
+
+lmp = lammps()
+me = lmp.extract_setting("world_rank")
+nprocs = lmp.extract_setting("world_size")
+
+# cubic diamond lattice constants 
+
+alat = 5.457
+
+# define the cubic diamond orthorhombic supercell
+# with 8 atoms
+
+basisstring = ""
+origin = np.zeros(3)
+bond = np.ones(3)*0.25
+b = origin
+basisstring += "basis %g %g %g " % (b[0],b[1],b[2])
+b = bond
+basisstring += "basis %g %g %g " % (b[0],b[1],b[2])
+
+for i in range(3):
+    b = 2*bond
+    b[i] = 0
+    basisstring += "basis %g %g %g " % (b[0],b[1],b[2])
+    b += bond
+    basisstring += "basis %g %g %g " % (b[0],b[1],b[2])
+
+hmat = np.eye(3)
+
+varlist = {
+    "logsuffix":"ortho",
+    "a":alat,
+    "a1x":hmat[0,0],
+    "a2x":hmat[0,1],
+    "a2y":hmat[1,1],
+    "a3x":hmat[0,2],
+    "a3y":hmat[1,2],
+    "a3z":hmat[2,2],
+    "l":alat,
+    "basis":basisstring,
+    "nlat":3,
+}
+
+cmdargs = gen_varargs(varlist)
+cij_ortho = calculate_cij(cmdargs)
+
+# define the cubic diamond triclinic primitive cell
+# with 2 atoms
+
+basisstring = ""
+origin = np.zeros(3)
+bond = np.ones(3)*0.25
+b = origin
+basisstring += "basis %g %g %g " % (b[0],b[1],b[2])
+b = bond
+basisstring += "basis %g %g %g " % (b[0],b[1],b[2])
+
+hmat1 = np.array([[1, 1, 0], [0, 1, 1], [1, 0, 1]]).T/np.sqrt(2)
+
+# rotate primitive cell to LAMMPS orientation
+# (upper triangular)
+
+qmat, rmat = np.linalg.qr(hmat1)
+ss = np.diagflat(np.sign(np.diag(rmat)))
+rot = ss @ qmat.T
+hmat2 = ss @ rmat
+
+varlist = {
+    "logsuffix":"tri",
+    "a":alat,
+    "a1x":hmat2[0,0],
+    "a2x":hmat2[0,1],
+    "a2y":hmat2[1,1],
+    "a3x":hmat2[0,2],
+    "a3y":hmat2[1,2],
+    "a3z":hmat2[2,2],
+    "l":alat/2**0.5,
+    "basis":basisstring,
+    "nlat":5,
+}
+
+cmdargs = gen_varargs(varlist)
+cij_tri = calculate_cij(cmdargs)
+
+if me == 0:
+    print("\nPython output:")
+    print("C_ortho = \n",cij_ortho)
+    print()
+    print("C_tri = \n",cij_tri)
+    print()
+
+    cij_tri_rot = rotate_cij(cij_tri, rot.T)
+
+    print("C_tri(rotated back) = \n",cij_tri_rot)
+    print()
+
+    print("C_ortho-C_tri = \n", cij_ortho-cij_tri_rot)
+    print()

examples/ELASTIC_T/BORN_MATRIX/Silicon/elastic_utils.py

@@ -0,0 +1,110 @@
+import numpy as np
+from lammps import lammps, LMP_VAR_EQUAL
+
+# method for rotating elastic constants
+
+def rotate_cij(cij, r):
+
+    # K_1
+    # R_11^2 R_12^2 R_13^2
+    # R_21^2 R_22^2 R_23^2
+    # R_31^2 R_32^2 R_33^2
+
+    k1 = r*r
+
+    # K_2
+    # R_12.R_13 R_13.R_11 R_11.R_12
+    # R_22.R_23 R_23.R_21 R_21.R_22
+    # R_32.R_33 R_33.R_31 R_31.R_32
+
+    k2 = np.array([
+        [r[0][1]*r[0][2], r[0][2]*r[0][0], r[0][0]*r[0][1]],
+        [r[1][1]*r[1][2], r[1][2]*r[1][0], r[1][0]*r[1][1]],
+        [r[2][1]*r[2][2], r[2][2]*r[2][0], r[2][0]*r[2][1]],
+    ])
+
+    # K_3
+    # R_21.R_31 R_22.R_32 R_23.R_33
+    # R_31.R_11 R_32.R_12 R_33.R_13
+    # R_11.R_21 R_12.R_22 R_13.R_23
+
+    k3 = np.array([
+        [r[1][0]*r[2][0], r[1][1]*r[2][1], r[1][2]*r[2][2]],
+        [r[2][0]*r[0][0], r[2][1]*r[0][1], r[2][2]*r[0][2]],
+        [r[0][0]*r[1][0], r[0][1]*r[1][1], r[0][2]*r[1][2]],
+    ])
+
+    # K_4a
+    # R_22.R_33 R_23.R_31 R_21.R_32
+    # R_32.R_13 R_33.R_11 R_31.R_12
+    # R_12.R_23 R_13.R_21 R_11.R_22
+
+    k4a = np.array([
+        [r[1][1]*r[2][2], r[1][2]*r[2][0], r[1][0]*r[2][1]],
+        [r[2][1]*r[0][2], r[2][2]*r[0][0], r[2][0]*r[0][1]],
+        [r[0][1]*r[1][2], r[0][2]*r[1][0], r[0][0]*r[1][1]],
+    ])
+
+    # K_4b
+    # R_23.R_32 R_21.R_33 R_22.R_31
+    # R_33.R_12 R_31.R_13 R_32.R_11
+    # R_13.R_22 R_11.R_23 R_12.R_21
+
+    k4b = np.array([
+        [r[1][2]*r[2][1], r[1][0]*r[2][2], r[1][1]*r[2][0]],
+        [r[2][2]*r[0][1], r[2][0]*r[0][2], r[2][1]*r[0][0]],
+        [r[0][2]*r[1][1], r[0][0]*r[1][2], r[0][1]*r[1][0]],
+    ])
+    
+    k = np.block([[k1, 2*k2],[k3, k4a+k4b]])
+    cijrot = k.dot(cij.dot(k.T))
+    return cijrot
+
+def calculate_cij(cmdargs):
+    lmp = lammps(cmdargs=cmdargs)
+    lmp.file("in.elastic")
+
+    C11 = lmp.extract_variable("C11",None, LMP_VAR_EQUAL)
+    C22 = lmp.extract_variable("C22",None, LMP_VAR_EQUAL)
+    C33 = lmp.extract_variable("C33",None, LMP_VAR_EQUAL)
+    C44 = lmp.extract_variable("C44",None, LMP_VAR_EQUAL)
+    C55 = lmp.extract_variable("C55",None, LMP_VAR_EQUAL)
+    C66 = lmp.extract_variable("C66",None, LMP_VAR_EQUAL)
+    
+    C12 = lmp.extract_variable("C12",None, LMP_VAR_EQUAL)
+    C13 = lmp.extract_variable("C13",None, LMP_VAR_EQUAL)
+    C14 = lmp.extract_variable("C14",None, LMP_VAR_EQUAL)
+    C15 = lmp.extract_variable("C15",None, LMP_VAR_EQUAL)
+    C16 = lmp.extract_variable("C16",None, LMP_VAR_EQUAL)
+    
+    C23 = lmp.extract_variable("C23",None, LMP_VAR_EQUAL)
+    C24 = lmp.extract_variable("C24",None, LMP_VAR_EQUAL)
+    C25 = lmp.extract_variable("C25",None, LMP_VAR_EQUAL)
+    C26 = lmp.extract_variable("C26",None, LMP_VAR_EQUAL)
+    
+    C34 = lmp.extract_variable("C34",None, LMP_VAR_EQUAL)
+    C35 = lmp.extract_variable("C35",None, LMP_VAR_EQUAL)
+    C36 = lmp.extract_variable("C36",None, LMP_VAR_EQUAL)
+    
+    C45 = lmp.extract_variable("C45",None, LMP_VAR_EQUAL)
+    C46 = lmp.extract_variable("C46",None, LMP_VAR_EQUAL)
+    
+    C56 = lmp.extract_variable("C56",None, LMP_VAR_EQUAL)
+
+    cij = np.array([
+      [C11, C12, C13, C14, C15, C16],
+      [  0, C22, C23, C24, C25, C26],
+      [  0,   0, C33, C34, C35, C36],
+      [  0,   0,   0, C44, C45, C46],
+      [  0,   0,   0,   0, C55, C56],
+      [  0,   0,   0,   0,   0, C66],
+    ])
+    cij = np.triu(cij) + np.tril(cij.T, -1)            
+
+    return cij
+
+def gen_varargs(varlist):
+    cmdargs = []
+    for key in varlist:
+        cmdargs += ["-var",key,str(varlist[key])]
+    return cmdargs

examples/ELASTIC_T/BORN_MATRIX/Silicon/init.in

@@ -1,13 +1,17 @@
 # NOTE: This script can be modified for different atomic structures, 
 # units, etc. See in.elastic for more info.
 #
-
 # Define MD parameters
 # These can be modified by the user
 # These settings replicate the 1477~K benchmark of
 # Kluge, Ray, and Rahman (1986) that is Ref.[15] in:
 # Y. Zhen, C. Chu, Computer Physics Communications 183(2012) 261-265
 
+# set log file
+
+variable logsuffix index ortho
+log log.elastic.${logsuffix}
+
 # select temperature and pressure (lattice constant)
 
 variable temp index 1477.0                 # temperature of initial sample
@@ -37,19 +41,34 @@ variable nrepeatborn equal floor(${nfreq}/${neveryborn}) # number of samples
 variable nequil equal 10*${nthermo}       # length of equilibration run
 variable nrun equal 100*${nthermo}        # length of equilibrated run
 
-# generate the box and atom positions using a diamond lattice
+# this generates a general triclinic cell
+# conforming to LAMMPS cell (upper triangular)
 
 units		metal
+box 		tilt large
 
-boundary	p p p
+# unit lattice vectors are
+# a1 = (a1x 0 0)
+# a2 = (a2x a2y 0)
+# a3 = (a3x a3y a3z)
 
-# this generates a standard 8-atom cubic cell
+variable        a1x index 1
+variable 	a2x index 0
+variable 	a2y index 1
+variable 	a3x index 0
+variable 	a3y index 0
+variable	a3z index 1
+variable	atmp equal $a
+variable 	l index $a
+variable	basis index "basis 0    0    0  basis 0.25 0.25 0.25 basis 0    0.5  0.5 basis 0.25 0.75 0.75 basis 0.5  0    0.5 basis 0.75 0.25 0.75 basis 0.5  0.5  0 basis 0.75 0.75 0.25"
+lattice         custom ${l}             &
+                a1 ${a1x}      0      0 &
+                a2 ${a2x} ${a2y}      0 &
+                a3 ${a3x} ${a3y} ${a3z} &
+                ${basis}    &
+		spacing 1 1 1
 
-lattice         diamond $a
-region		box prism 0 1 0 1 0 1 0 0 0
-
-# this generates a 2-atom triclinic cell
-#include tri.in
+region		box prism 0 ${a1x} 0 ${a2y} 0 ${a3z} ${a2x} ${a3x} ${a3y}
 
 create_box	1 box
 create_atoms	1 box
@@ -57,3 +76,4 @@ mass 1 ${mass1}
 replicate ${nlat} ${nlat} ${nlat}
 velocity	all create ${temp} 87287
 
+

examples/ELASTIC_T/BORN_MATRIX/Silicon/log.16May22.ortho.g++.4

@@ -0,0 +1,662 @@
+
+# select temperature and pressure (lattice constant)
+
+variable temp index 1477.0                 # temperature of initial sample
+variable a index 5.457                     # lattice constant
+
+# select sampling parameters, important for speed/convergence
+
+variable nthermo index 1500               # interval for thermo output
+variable nevery index 10                  # stress sampling interval
+variable neveryborn index 100             # Born sampling interval
+variable timestep index 0.000766          # timestep
+variable nlat index 3                     # number of lattice unit cells
+
+# other settings
+
+variable mass1 index 28.06                # mass
+variable tdamp index 0.01                 # time constant for thermostat
+variable seed index 123457                # seed for thermostat
+variable thermostat index 1               # 0 if NVE, 1 if NVT
+variable delta index 1.0e-6               # Born numdiff strain magnitude
+
+# hard-coded rules-of-thumb for run length, etc.
+
+variable nfreq equal ${nthermo}           # interval for averaging output
+variable nfreq equal 1500           
+variable nrepeat equal floor(${nfreq}/${nevery}) # number of samples
+variable nrepeat equal floor(1500/${nevery}) 
+variable nrepeat equal floor(1500/10) 
+variable nrepeatborn equal floor(${nfreq}/${neveryborn}) # number of samples
+variable nrepeatborn equal floor(1500/${neveryborn}) 
+variable nrepeatborn equal floor(1500/100) 
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nequil equal 10*1500       
+variable nrun equal 100*${nthermo}        # length of equilibrated run
+variable nrun equal 100*1500        
+
+# this generates a general triclinic cell
+# conforming to LAMMPS cell (upper triangular)
+
+units		metal
+box 		tilt large
+
+# unit lattice vectors are
+# a1 = (a1x 0 0)
+# a2 = (a2x a2y 0)
+# a3 = (a3x a3y a3z)
+
+variable        a1x index 1
+variable 	a2x index 0
+variable 	a2y index 1
+variable 	a3x index 0
+variable 	a3y index 0
+variable	a3z index 1
+variable	atmp equal $a
+variable	atmp equal 5.457
+variable 	l index $a
+variable 	l index 5.457
+variable	basis index "basis 0    0    0  basis 0.25 0.25 0.25 basis 0    0.5  0.5 basis 0.25 0.75 0.75 basis 0.5  0    0.5 basis 0.75 0.25 0.75 basis 0.5  0.5  0 basis 0.75 0.75 0.25"
+lattice         custom ${l}                             a1 ${a1x}      0      0                 a2 ${a2x} ${a2y}      0                 a3 ${a3x} ${a3y} ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 5.457                             a1 ${a1x}      0      0                 a2 ${a2x} ${a2y}      0                 a3 ${a3x} ${a3y} ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 5.457                             a1 1.0      0      0                 a2 ${a2x} ${a2y}      0                 a3 ${a3x} ${a3y} ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 5.457                             a1 1.0      0      0                 a2 0.0 ${a2y}      0                 a3 ${a3x} ${a3y} ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 5.457                             a1 1.0      0      0                 a2 0.0 1.0      0                 a3 ${a3x} ${a3y} ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 5.457                             a1 1.0      0      0                 a2 0.0 1.0      0                 a3 0.0 ${a3y} ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 5.457                             a1 1.0      0      0                 a2 0.0 1.0      0                 a3 0.0 0.0 ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 5.457                             a1 1.0      0      0                 a2 0.0 1.0      0                 a3 0.0 0.0 1.0                 ${basis}    		spacing 1 1 1
+lattice         custom 5.457                             a1 1.0      0      0                 a2 0.0 1.0      0                 a3 0.0 0.0 1.0                 basis 0 0 0 basis 0.25 0.25 0.25 basis 0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0 basis 0.75 0.75 0.25     		spacing 1 1 1
+Lattice spacing in x,y,z = 5.457 5.457 5.457
+
+region		box prism 0 ${a1x} 0 ${a2y} 0 ${a3z} ${a2x} ${a3x} ${a3y}
+region		box prism 0 1.0 0 ${a2y} 0 ${a3z} ${a2x} ${a3x} ${a3y}
+region		box prism 0 1.0 0 1.0 0 ${a3z} ${a2x} ${a3x} ${a3y}
+region		box prism 0 1.0 0 1.0 0 1.0 ${a2x} ${a3x} ${a3y}
+region		box prism 0 1.0 0 1.0 0 1.0 0.0 ${a3x} ${a3y}
+region		box prism 0 1.0 0 1.0 0 1.0 0.0 0.0 ${a3y}
+region		box prism 0 1.0 0 1.0 0 1.0 0.0 0.0 0.0
+
+create_box	1 box
+Created triclinic box = (0 0 0) to (5.457 5.457 5.457) with tilt (0 0 0)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 8 atoms
+  using lattice units in triclinic box = (0 0 0) to (5.457 5.457 5.457) with tilt (0 0 0)
+  create_atoms CPU = 0.000 seconds
+mass 1 ${mass1}
+mass 1 28.06
+replicate ${nlat} ${nlat} ${nlat}
+replicate 3 ${nlat} ${nlat}
+replicate 3 3 ${nlat}
+replicate 3 3 3
+Replicating atoms ...
+  triclinic box = (0 0 0) to (16.371 16.371 16.371) with tilt (0 0 0)
+  1 by 2 by 2 MPI processor grid
+  216 atoms
+  replicate CPU = 0.001 seconds
+velocity	all create ${temp} 87287
+velocity	all create 1477.0 87287
+
+
+
+# Compute initial state
+
+include potential.in
+# NOTE: This script can be modified for different pair styles
+# See in.elastic for more info.
+
+reset_timestep 0
+
+# Choose potential
+pair_style	sw
+pair_coeff * * Si.sw Si
+Reading sw potential file Si.sw with DATE: 2007-06-11
+
+# Setup neighbor style
+neighbor 1.0 nsq
+neigh_modify once no every 1 delay 0 check yes
+
+# Setup MD
+
+timestep ${timestep}
+timestep 0.000766
+fix 4 all nve
+if "${thermostat} == 1" then    "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}
+fix 5 all langevin 1477.0 ${temp} ${tdamp} ${seed}
+fix 5 all langevin 1477.0 1477.0 ${tdamp} ${seed}
+fix 5 all langevin 1477.0 1477.0 0.01 ${seed}
+fix 5 all langevin 1477.0 1477.0 0.01 123457
+
+
+thermo_style custom step temp pe press density
+run ${nequil}
+run 15000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.77118
+  ghost atom cutoff = 4.77118
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sw, perpetual
+      attributes: full, newton on
+      pair build: full/nsq
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.053 | 3.053 | 3.053 Mbytes
+   Step          Temp          PotEng         Press         Density    
+         0   1477          -936.42473     -4264.7155      2.2938491    
+     15000   1409.2705     -887.74266     -595.80958      2.2938491    
+Loop time of 1.46866 on 4 procs for 15000 steps with 216 atoms
+
+Performance: 675.949 ns/day, 0.036 hours/ns, 10213.420 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.1178     | 1.1422     | 1.167      |   1.8 | 77.77
+Neigh   | 0.015423   | 0.015665   | 0.015835   |   0.1 |  1.07
+Comm    | 0.24267    | 0.26778    | 0.2925     |   3.8 | 18.23
+Output  | 1.2863e-05 | 1.4971e-05 | 2.0888e-05 |   0.0 |  0.00
+Modify  | 0.019642   | 0.020192   | 0.020638   |   0.3 |  1.37
+Other   |            | 0.02277    |            |       |  1.55
+
+Nlocal:             54 ave          56 max          50 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost:            353 ave         357 max         351 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:       1423.5 ave        1487 max        1324 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+
+Total # of neighbors = 5694
+Ave neighs/atom = 26.361111
+Neighbor list builds = 251
+Dangerous builds = 0
+
+# Run dynamics
+
+include potential.in
+# NOTE: This script can be modified for different pair styles
+# See in.elastic for more info.
+
+reset_timestep 0
+
+# Choose potential
+pair_style	sw
+pair_coeff * * Si.sw Si
+Reading sw potential file Si.sw with DATE: 2007-06-11
+
+# Setup neighbor style
+neighbor 1.0 nsq
+neigh_modify once no every 1 delay 0 check yes
+
+# Setup MD
+
+timestep ${timestep}
+timestep 0.000766
+fix 4 all nve
+if "${thermostat} == 1" then    "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}
+fix 5 all langevin 1477.0 ${temp} ${tdamp} ${seed}
+fix 5 all langevin 1477.0 1477.0 ${tdamp} ${seed}
+fix 5 all langevin 1477.0 1477.0 0.01 ${seed}
+fix 5 all langevin 1477.0 1477.0 0.01 123457
+
+
+include output.in
+# Setup output
+
+# Stress fluctuation term F
+
+compute stress all pressure thermo_temp
+variable s1 equal c_stress[1]
+variable s2 equal c_stress[2]
+variable s3 equal c_stress[3]
+variable s4 equal c_stress[6]
+variable s5 equal c_stress[5]
+variable s6 equal c_stress[4]
+
+variable s11 equal v_s1*v_s1
+variable s22 equal v_s2*v_s2
+variable s33 equal v_s3*v_s3
+variable s44 equal v_s4*v_s4
+variable s55 equal v_s5*v_s5
+variable s66 equal v_s6*v_s6
+variable s33 equal v_s3*v_s3
+variable s12 equal v_s1*v_s2
+variable s13 equal v_s1*v_s3
+variable s14 equal v_s1*v_s4
+variable s15 equal v_s1*v_s5
+variable s16 equal v_s1*v_s6
+variable s23 equal v_s2*v_s3
+variable s24 equal v_s2*v_s4
+variable s25 equal v_s2*v_s5
+variable s26 equal v_s2*v_s6
+variable s34 equal v_s3*v_s4
+variable s35 equal v_s3*v_s5
+variable s36 equal v_s3*v_s6
+variable s45 equal v_s4*v_s5
+variable s46 equal v_s4*v_s6
+variable s56 equal v_s5*v_s6
+
+variable mytemp equal temp
+variable mypress equal press
+variable mype equal pe/atoms
+fix avt all ave/time ${nevery} ${nrepeat} ${nfreq} v_mytemp ave running
+fix avt all ave/time 10 ${nrepeat} ${nfreq} v_mytemp ave running
+fix avt all ave/time 10 150 ${nfreq} v_mytemp ave running
+fix avt all ave/time 10 150 1500 v_mytemp ave running
+fix avp all ave/time ${nevery} ${nrepeat} ${nfreq} v_mypress ave running
+fix avp all ave/time 10 ${nrepeat} ${nfreq} v_mypress ave running
+fix avp all ave/time 10 150 ${nfreq} v_mypress ave running
+fix avp all ave/time 10 150 1500 v_mypress ave running
+fix avpe all ave/time ${nevery} ${nrepeat} ${nfreq} v_mype ave running
+fix avpe all ave/time 10 ${nrepeat} ${nfreq} v_mype ave running
+fix avpe all ave/time 10 150 ${nfreq} v_mype ave running
+fix avpe all ave/time 10 150 1500 v_mype ave running
+fix avs all ave/time ${nevery} ${nrepeat} ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
+fix avs all ave/time 10 ${nrepeat} ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
+fix avs all ave/time 10 150 ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
+fix avs all ave/time 10 150 1500 v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
+fix avssq all ave/time ${nevery} ${nrepeat} ${nfreq} v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
+fix avssq all ave/time 10 ${nrepeat} ${nfreq} v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
+fix avssq all ave/time 10 150 ${nfreq} v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
+fix avssq all ave/time 10 150 1500 v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
+
+# bar to GPa
+variable pconv equal 1.0e5/1.0e9
+variable cunits index GPa
+# metal unit constants from LAMMPS
+# force->nktv2p = 1.6021765e6;
+# force->boltz = 8.617343e-5;
+variable boltz equal 8.617343e-5
+variable nktv2p equal 1.6021765e6
+variable vkt equal vol/(${boltz}*${temp})/${nktv2p}
+variable vkt equal vol/(8.617343e-05*${temp})/${nktv2p}
+variable vkt equal vol/(8.617343e-05*1477.0)/${nktv2p}
+variable vkt equal vol/(8.617343e-05*1477.0)/1602176.5
+variable ffac equal ${pconv}*${vkt}
+variable ffac equal 0.0001*${vkt}
+variable ffac equal 0.0001*0.0215159929384811
+
+variable F11 equal -(f_avssq[1]-f_avs[1]*f_avs[1])*${ffac}
+variable F11 equal -(f_avssq[1]-f_avs[1]*f_avs[1])*2.15159929384811e-06
+variable F22 equal -(f_avssq[2]-f_avs[2]*f_avs[2])*${ffac}
+variable F22 equal -(f_avssq[2]-f_avs[2]*f_avs[2])*2.15159929384811e-06
+variable F33 equal -(f_avssq[3]-f_avs[3]*f_avs[3])*${ffac}
+variable F33 equal -(f_avssq[3]-f_avs[3]*f_avs[3])*2.15159929384811e-06
+variable F44 equal -(f_avssq[4]-f_avs[4]*f_avs[4])*${ffac}
+variable F44 equal -(f_avssq[4]-f_avs[4]*f_avs[4])*2.15159929384811e-06
+variable F55 equal -(f_avssq[5]-f_avs[5]*f_avs[5])*${ffac}
+variable F55 equal -(f_avssq[5]-f_avs[5]*f_avs[5])*2.15159929384811e-06
+variable F66 equal -(f_avssq[6]-f_avs[6]*f_avs[6])*${ffac}
+variable F66 equal -(f_avssq[6]-f_avs[6]*f_avs[6])*2.15159929384811e-06
+
+variable F12 equal -(f_avssq[7]-f_avs[1]*f_avs[2])*${ffac}
+variable F12 equal -(f_avssq[7]-f_avs[1]*f_avs[2])*2.15159929384811e-06
+variable F13 equal -(f_avssq[8]-f_avs[1]*f_avs[3])*${ffac}
+variable F13 equal -(f_avssq[8]-f_avs[1]*f_avs[3])*2.15159929384811e-06
+variable F14 equal -(f_avssq[9]-f_avs[1]*f_avs[4])*${ffac}
+variable F14 equal -(f_avssq[9]-f_avs[1]*f_avs[4])*2.15159929384811e-06
+variable F15 equal -(f_avssq[10]-f_avs[1]*f_avs[5])*${ffac}
+variable F15 equal -(f_avssq[10]-f_avs[1]*f_avs[5])*2.15159929384811e-06
+variable F16 equal -(f_avssq[11]-f_avs[1]*f_avs[6])*${ffac}
+variable F16 equal -(f_avssq[11]-f_avs[1]*f_avs[6])*2.15159929384811e-06
+
+variable F23 equal -(f_avssq[12]-f_avs[2]*f_avs[3])*${ffac}
+variable F23 equal -(f_avssq[12]-f_avs[2]*f_avs[3])*2.15159929384811e-06
+variable F24 equal -(f_avssq[13]-f_avs[2]*f_avs[4])*${ffac}
+variable F24 equal -(f_avssq[13]-f_avs[2]*f_avs[4])*2.15159929384811e-06
+variable F25 equal -(f_avssq[14]-f_avs[2]*f_avs[5])*${ffac}
+variable F25 equal -(f_avssq[14]-f_avs[2]*f_avs[5])*2.15159929384811e-06
+variable F26 equal -(f_avssq[15]-f_avs[2]*f_avs[6])*${ffac}
+variable F26 equal -(f_avssq[15]-f_avs[2]*f_avs[6])*2.15159929384811e-06
+
+variable F34 equal -(f_avssq[16]-f_avs[3]*f_avs[4])*${ffac}
+variable F34 equal -(f_avssq[16]-f_avs[3]*f_avs[4])*2.15159929384811e-06
+variable F35 equal -(f_avssq[17]-f_avs[3]*f_avs[5])*${ffac}
+variable F35 equal -(f_avssq[17]-f_avs[3]*f_avs[5])*2.15159929384811e-06
+variable F36 equal -(f_avssq[18]-f_avs[3]*f_avs[6])*${ffac}
+variable F36 equal -(f_avssq[18]-f_avs[3]*f_avs[6])*2.15159929384811e-06
+
+variable F45 equal -(f_avssq[19]-f_avs[4]*f_avs[5])*${ffac}
+variable F45 equal -(f_avssq[19]-f_avs[4]*f_avs[5])*2.15159929384811e-06
+variable F46 equal -(f_avssq[20]-f_avs[4]*f_avs[6])*${ffac}
+variable F46 equal -(f_avssq[20]-f_avs[4]*f_avs[6])*2.15159929384811e-06
+
+variable F56 equal -(f_avssq[21]-f_avs[5]*f_avs[6])*${ffac}
+variable F56 equal -(f_avssq[21]-f_avs[5]*f_avs[6])*2.15159929384811e-06
+
+# Born term
+
+compute     virial all pressure NULL virial
+compute     born all born/matrix numdiff ${delta} virial
+compute     born all born/matrix numdiff 1.0e-6 virial
+fix 	    avborn all ave/time ${neveryborn} ${nrepeatborn} ${nfreq} c_born[*] ave running
+fix 	    avborn all ave/time 100 ${nrepeatborn} ${nfreq} c_born[*] ave running
+fix 	    avborn all ave/time 100 15 ${nfreq} c_born[*] ave running
+fix 	    avborn all ave/time 100 15 1500 c_born[*] ave running
+
+variable bfac equal ${pconv}*${nktv2p}/vol
+variable bfac equal 0.0001*${nktv2p}/vol
+variable bfac equal 0.0001*1602176.5/vol
+variable B vector f_avborn*${bfac}
+variable B vector f_avborn*0.036516128938577
+
+# Kinetic term
+
+variable kfac equal ${pconv}*${nktv2p}*atoms*${boltz}*${temp}/vol
+variable kfac equal 0.0001*${nktv2p}*atoms*${boltz}*${temp}/vol
+variable kfac equal 0.0001*1602176.5*atoms*${boltz}*${temp}/vol
+variable kfac equal 0.0001*1602176.5*atoms*8.617343e-05*${temp}/vol
+variable kfac equal 0.0001*1602176.5*atoms*8.617343e-05*1477.0/vol
+variable K11 equal 4.0*${kfac}
+variable K11 equal 4.0*1.00390440086865
+variable K22 equal 4.0*${kfac}
+variable K22 equal 4.0*1.00390440086865
+variable K33 equal 4.0*${kfac}
+variable K33 equal 4.0*1.00390440086865
+variable K44 equal 2.0*${kfac}
+variable K44 equal 2.0*1.00390440086865
+variable K55 equal 2.0*${kfac}
+variable K55 equal 2.0*1.00390440086865
+variable K66 equal 2.0*${kfac}
+variable K66 equal 2.0*1.00390440086865
+
+# Add F, K, and B together
+
+variable C11 equal v_F11+v_B[1]+v_K11
+variable C22 equal v_F22+v_B[2]+v_K22
+variable C33 equal v_F33+v_B[3]+v_K33
+variable C44 equal v_F44+v_B[4]+v_K44
+variable C55 equal v_F55+v_B[5]+v_K55
+variable C66 equal v_F66+v_B[6]+v_K66
+
+variable C12 equal v_F12+v_B[7]
+variable C13 equal v_F13+v_B[8]
+variable C14 equal v_F14+v_B[9]
+variable C15 equal v_F15+v_B[10]
+variable C16 equal v_F16+v_B[11]
+
+variable C23 equal v_F23+v_B[12]
+variable C24 equal v_F24+v_B[13]
+variable C25 equal v_F25+v_B[14]
+variable C26 equal v_F26+v_B[15]
+
+variable C34 equal v_F34+v_B[16]
+variable C35 equal v_F35+v_B[17]
+variable C36 equal v_F36+v_B[18]
+
+variable C45 equal v_F45+v_B[19]
+variable C46 equal v_F46+v_B[20]
+
+variable C56 equal v_F56+v_B[21]
+
+thermo		${nthermo}
+thermo		1500
+thermo_style custom step temp pe press density f_avt f_avp f_avpe v_F11 v_F22 v_F33 v_F44 v_F55 v_F66 v_F12 v_F13 v_F23 v_B[*8] v_B[12]
+
+thermo_modify norm no
+
+run ${nrun}
+run 150000
+Per MPI rank memory allocation (min/avg/max) = 3.803 | 3.803 | 3.803 Mbytes
+   Step          Temp          PotEng         Press         Density         f_avt          f_avp          f_avpe         v_F11          v_F22          v_F33          v_F44          v_F55          v_F66          v_F12          v_F13          v_F23          v_B[1]         v_B[2]         v_B[3]         v_B[4]         v_B[5]         v_B[6]         v_B[7]         v_B[8]        v_B[12]    
+         0   1409.2705     -887.74266     -595.80958      2.2938491      0              0              0             -0             -0             -0             -0             -0             -0             -0             -0             -0              0              0              0              0              0              0              0              0              0            
+      1500   1543.955      -894.59564      829.29754      2.2938491      1479.8455     -272.48983     -4.1286994     -9.8546328     -7.6109829     -6.9399455     -42.917041     -50.311599     -54.999307     -2.1718852     -0.37897892     0.021065401    136.52661      136.57057      136.8112       99.817258      99.81304       99.70618       74.718855      74.984867      74.922489    
+      3000   1533.4697     -891.05441      1291.5832      2.2938491      1482.4036     -135.16653     -4.130281      -8.5756153     -7.6746515     -7.0427547     -50.764257     -49.209172     -60.778328     -1.3700831     -0.4568356      0.20721573     136.58667      136.70561      136.69409      99.903478      99.76887       99.847801      74.700603      74.769035      74.913031    
+      4500   1559.2333     -895.95898     -169.5185       2.2938491      1481.5554      110.86891     -4.1325482     -8.0338125     -7.6953586     -7.3762168     -53.430221     -48.29504      -54.657257     -1.3016296     -1.0260182     -0.045906996    136.84569      136.91821      136.90927      100.0598       99.901964      100.07314      74.813284      74.723978      74.90986     
+      6000   1417.6434     -891.85991      84.448937      2.2938491      1480.5364     -26.042555     -4.130823      -8.2176554     -7.6691593     -7.5195046     -54.897719     -45.58593      -53.146497     -1.1159385     -0.4148108     -0.34277881     136.73272      136.74579      136.70656      99.899987      99.788575      99.91922       74.858104      74.751356      74.877807    
+      7500   1521.8549     -890.45085     -1986.131       2.2938491      1478.7883     -63.188659     -4.131248      -7.9884217     -7.5621903     -7.6827376     -53.505647     -51.167165     -54.069643     -1.0788226     -0.72907125    -0.40595255     136.65015      136.58541      136.66316      99.849936      99.770641      99.833465      74.762105      74.749673      74.793725    
+      9000   1481.1098     -893.58876     -302.11196      2.2938491      1480.8996     -86.706608     -4.1308352     -7.8504102     -7.4016325     -7.7875364     -52.129057     -50.748636     -55.590171     -1.0423024     -1.0411667     -0.42332136     136.61748      136.54744      136.63721      99.806859      99.750078      99.824904      74.793868      74.742871      74.75755     
+     10500   1602.1539     -891.59953     -120.50983      2.2938491      1481.8078     -58.72234      -4.1309965     -7.979615      -7.4378227     -7.6187667     -51.499039     -50.360191     -52.483908     -0.79006562    -0.97184735    -0.42288111     136.62376      136.57134      136.65198      99.809774      99.788741      99.818781      74.780283      74.754346      74.752685    
+     12000   1419.1584     -891.48511     -357.00507      2.2938491      1482.0565     -52.541967     -4.1307476     -7.8017302     -7.3965439     -7.5326968     -51.907957     -50.643325     -53.453282     -0.84401937    -1.0517326     -0.54021711     136.58968      136.54882      136.65563      99.810907      99.792391      99.770152      74.770444      74.788526      74.767629    
+     13500   1349.3981     -893.65888      15.31558       2.2938491      1481.1263     -55.35676      -4.1307105     -7.5797633     -7.3093859     -7.5484467     -52.298219     -49.804373     -54.555982     -0.8242492     -1.0633311     -0.58879705     136.59553      136.58666      136.66121      99.806084      99.807326      99.79773       74.783157      74.799104      74.776677    
+     15000   1572.7545     -888.05032     -1167.1259      2.2938491      1481.1845     -44.051939     -4.1307308     -7.4870604     -7.3959358     -7.7984973     -53.846519     -49.850023     -54.449806     -0.80437631    -0.98162577    -0.67631044     136.6089       136.60586      136.63322      99.804941      99.816756      99.807316      74.799246      74.79994       74.774964    
+     16500   1476.3559     -894.13606     -141.71585      2.2938491      1481.9977     -57.149347     -4.1305532     -7.3563308     -7.7377027     -7.7801895     -55.418093     -50.432917     -55.092322     -0.75882435    -0.91155917    -0.8012947      136.60588      136.59648      136.64052      99.783788      99.813543      99.811844      74.796195      74.795566      74.759748    
+     18000   1385.3464     -894.17196     -453.51135      2.2938491      1482.2841     -41.202526     -4.1305936     -7.4001985     -7.9100844     -7.7977726     -55.828868     -51.190641     -56.146338     -0.80951377    -0.88498405    -0.95870035     136.60877      136.58913      136.64391      99.807809      99.807278      99.804971      74.795414      74.787039      74.770228    
+     19500   1459.0464     -891.56293     -583.43289      2.2938491      1481.6087     -80.19681      -4.1305727     -7.503849      -7.832224      -8.0680015     -55.621765     -52.943951     -55.834411     -0.84395931    -0.92355108    -1.0598691      136.57225      136.54527      136.59315      99.781928      99.757893      99.808931      74.802468      74.747248      74.742414    
+     21000   1425.7724     -893.96346     -2476.1354      2.2938491      1480.7898     -80.510469     -4.1307098     -7.5517651     -7.7540688     -8.1263923     -55.676836     -51.985142     -57.190698     -0.79979707    -0.82062764    -0.96974038     136.62238      136.56316      136.58301      99.770462      99.774612      99.833221      74.817335      74.767434      74.729171    
+     22500   1478.3908     -893.03263      356.73894      2.2938491      1481.8216     -56.608103     -4.1307548     -7.5171851     -7.7473191     -8.1531481     -55.174277     -52.991179     -56.943478     -0.83236889    -0.86233325    -0.84237825     136.63109      136.54755      136.58015      99.768999      99.789091      99.834769      74.805682      74.762367      74.709251    
+     24000   1559.2834     -895.0061       408.35518      2.2938491      1481.7034     -50.365601     -4.1310012     -7.4371076     -7.6686437     -8.0973363     -55.391365     -53.957438     -56.758804     -0.75624259    -0.7712068     -0.79151732     136.63369      136.569        136.62933      99.801995      99.811857      99.834171      74.784642      74.764728      74.726548    
+     25500   1418.8679     -900.05172      1038.8634      2.2938491      1481.7117     -34.795555     -4.1311417     -7.3525995     -7.6549985     -8.0932453     -55.209186     -54.850159     -56.555154     -0.76945854    -0.80520239    -0.87729866     136.65191      136.56496      136.6234       99.797985      99.83181       99.845733      74.777288      74.761405      74.70467     
+     27000   1337.6729     -892.54371     -1223.1078      2.2938491      1481.7999     -6.868253      -4.1314105     -7.4344069     -7.670465      -8.0748588     -55.642919     -54.694351     -56.043818     -0.84229089    -0.85050448    -0.8848331      136.69353      136.58737      136.65353      99.816588      99.854571      99.87065       74.779124      74.767968      74.713918    
+     28500   1428.3391     -890.39992      1637.2396      2.2938491      1481.456      -5.7648513     -4.1315226     -7.401319      -7.6104928     -8.0522046     -55.924803     -54.963031     -55.354755     -0.80198132    -0.78513105    -0.89948604     136.66669      136.57056      136.6591       99.824707      99.851902      99.853954      74.769147      74.764532      74.720065    
+     30000   1610.749      -892.10736      579.88182      2.2938491      1480.9008      6.256216      -4.1316122     -7.4537451     -7.5486694     -7.9515037     -56.204342     -55.065875     -55.139775     -0.83945753    -0.80897524    -0.84944598     136.67155      136.59361      136.64942      99.830699      99.848762      99.869963      74.777778      74.755753      74.718528    
+     31500   1424.0387     -892.82589     -1088.8668      2.2938491      1480.8612      27.560648     -4.1318123     -7.4239872     -7.5434979     -7.8962752     -56.813306     -55.891849     -55.592699     -0.90786211    -0.78634826    -0.89364109     136.67764      136.59992      136.66244      99.844569      99.867062      99.872844      74.758315      74.7448        74.710189    
+     33000   1608.6242     -892.4438       2546.9882      2.2938491      1481.6562      47.051547     -4.1316992     -7.4646486     -7.5038235     -7.8961468     -57.865394     -55.375621     -56.027867     -0.8910679     -0.84053561    -0.89582173     136.68768      136.59732      136.67152      99.846034      99.880097      99.867468      74.752249      74.751739      74.710642    
+     34500   1459.0403     -892.25499      551.36057      2.2938491      1482.1308      44.660322     -4.1317055     -7.4352078     -7.5237108     -7.8649773     -58.468947     -55.357512     -55.779494     -0.84115908    -0.77476537    -0.87458546     136.66595      136.59551      136.65084      99.839323      99.866733      99.8611        74.741493      74.738738      74.709871    
+     36000   1421.5526     -896.28506     -29.316911      2.2938491      1481.789       47.541032     -4.1318408     -7.3733107     -7.5190295     -7.8143454     -57.929804     -55.418333     -55.785571     -0.83611043    -0.73869976    -0.86057781     136.67194      136.61145      136.66484      99.85524       99.874475      99.868689      74.735031      74.73536       74.716839    
+     37500   1420.8916     -891.82782     -124.77618      2.2938491      1481.4989      50.677557     -4.1319034     -7.351484      -7.4418106     -7.8130188     -57.428955     -55.290755     -55.728856     -0.79501628    -0.76420281    -0.87517695     136.6581       136.61188      136.65931      99.8659        99.870608      99.861288      74.723088      74.734658      74.717       
+     39000   1419.8533     -891.85187      775.65186      2.2938491      1481.3759      61.485208     -4.1320474     -7.3143703     -7.3968445     -7.781877      -57.264431     -55.699481     -55.805103     -0.76748846    -0.78919404    -0.83311458     136.66482      136.61272      136.64292      99.859449      99.871369      99.879933      74.724309      74.716924      74.690243    
+     40500   1618.5121     -891.22453      478.34407      2.2938491      1481.7031      51.968148     -4.1319722     -7.2819086     -7.5511556     -7.7257743     -57.306557     -55.743925     -56.312823     -0.83338334    -0.78815013    -0.80988519     136.65567      136.58905      136.64007      99.843268      99.870939      99.865104      74.716829      74.725634      74.69278     
+     42000   1532.044      -890.39164      1505.0844      2.2938491      1482.0334      59.439461     -4.1318795     -7.2758088     -7.601243      -7.6989373     -57.29647      -55.736173     -55.983442     -0.84537078    -0.77684239    -0.7910269      136.65858      136.5908       136.64401      99.845607      99.869513      99.867281      74.724164      74.732279      74.699567    
+     43500   1390.2967     -890.21856      1078.0917      2.2938491      1482.3754      56.694555     -4.1317225     -7.2485872     -7.568553      -7.7195095     -57.819566     -55.528042     -55.848214     -0.82149712    -0.82258095    -0.75292757     136.66772      136.57379      136.65372      99.83762       99.882723      99.854263      74.72191       74.747558      74.704137    
+     45000   1427.5782     -892.18995     -564.57357      2.2938491      1482.0054      64.751105     -4.1319259     -7.2234655     -7.5860705     -7.6146702     -57.745852     -56.095471     -55.618665     -0.77244466    -0.77811125    -0.75729958     136.66838      136.59611      136.6615       99.853922      99.886483      99.864469      74.715773      74.736269      74.702744    
+     46500   1457.907      -890.87371      1296.2125      2.2938491      1481.9658      74.963993     -4.1319725     -7.2288448     -7.5807903     -7.6640053     -57.821382     -55.848166     -55.521503     -0.80230061    -0.78832769    -0.77589289     136.69039      136.61343      136.68259      99.862454      99.896917      99.881487      74.726406      74.741295      74.710053    
+     48000   1526.0771     -895.53336      951.53234      2.2938491      1481.7295      84.065637     -4.1320813     -7.2137393     -7.545201      -7.6839878     -57.914627     -55.591336     -55.900718     -0.79496608    -0.78179316    -0.79496022     136.6987       136.62461      136.70778      99.879775      99.908913      99.883958      74.71782       74.746229      74.714358    
+     49500   1657.943      -890.09268      424.53616      2.2938491      1481.5972      95.06808      -4.1322261     -7.2312162     -7.5609924     -7.6933969     -58.460164     -55.614895     -55.68435      -0.7539777     -0.78036417    -0.84398343     136.70672      136.6326       136.70523      99.887231      99.910615      99.890981      74.711921      74.735306      74.70572     
+     51000   1517.8791     -894.6926       1412.5634      2.2938491      1481.8411      91.241557     -4.1321301     -7.2856849     -7.554417      -7.6852066     -58.824904     -55.906732     -55.722124     -0.72652169    -0.74459334    -0.824857       136.70149      136.63447      136.70155      99.892122      99.901377      99.890263      74.713234      74.73149       74.710717    
+     52500   1546.6245     -895.29958      181.50897      2.2938491      1482.1091      82.209025     -4.132121      -7.2711566     -7.5656939     -7.6600316     -58.75721      -55.971266     -55.724274     -0.72068642    -0.74174146    -0.81673789     136.68292      136.62513      136.69226      99.883717      99.900635      99.877994      74.704983      74.724386      74.708085    
+     54000   1432.5143     -892.33522     -1007.7153      2.2938491      1481.7799      82.064986     -4.1320527     -7.2297435     -7.5532463     -7.5873553     -58.769531     -56.753962     -55.320358     -0.69093494    -0.71376103    -0.8266532      136.66681      136.62772      136.68861      99.880916      99.890283      99.87535       74.709314      74.72301       74.713722    
+     55500   1525.2554     -890.36734      1294.5154      2.2938491      1481.5565      85.222591     -4.1321435     -7.2322453     -7.5028572     -7.5979369     -58.470473     -56.91003      -54.983461     -0.67325171    -0.68237059    -0.82452296     136.68218      136.64126      136.71384      99.888262      99.903988      99.885655      74.709774      74.736014      74.716975    
+     57000   1480.851      -891.41709     -148.33291      2.2938491      1481.401       80.316901     -4.1321436     -7.262647      -7.5256821     -7.6034232     -58.185727     -56.55166      -54.966948     -0.69905198    -0.64380996    -0.84814546     136.677        136.64844      136.7165       99.891933      99.904202      99.884534      74.70914       74.736681      74.716403    
+     58500   1546.9102     -892.66057      1089.3405      2.2938491      1481.4299      78.801721     -4.1321113     -7.276498      -7.5191946     -7.617463      -58.32857      -56.257777     -54.959089     -0.67949464    -0.65491266    -0.85310199     136.67479      136.64503      136.70605      99.885427      99.899987      99.884663      74.714168      74.737379      74.714314    
+     60000   1485.6648     -893.08278     -428.03608      2.2938491      1481.7631      79.689946     -4.1321441     -7.2552452     -7.5131486     -7.57811       -58.354213     -56.020669     -55.063017     -0.69757949    -0.6589713     -0.84658488     136.67189      136.63503      136.69828      99.877882      99.900844      99.87896       74.707924      74.735972      74.703597    
+     61500   1495.0662     -890.78023      1028.7889      2.2938491      1481.9678      75.884372     -4.1320422     -7.2080989     -7.5371914     -7.5381901     -58.053737     -56.190462     -55.148238     -0.69885347    -0.63670212    -0.87555185     136.65839      136.62158      136.68603      99.869396      99.894708      99.868716      74.704861      74.735992      74.700569    
+     63000   1409.6818     -887.95961     -1304.652       2.2938491      1482.3126      76.410022     -4.1319825     -7.2523905     -7.5152373     -7.5536513     -58.73159      -56.137578     -54.799791     -0.73461753    -0.67809249    -0.88492027     136.65593      136.62329      136.67831      99.868652      99.888176      99.869266      74.703693      74.730048      74.701284    
+     64500   1582.31       -895.49087      1119.2594      2.2938491      1482.1186      66.626242     -4.1320087     -7.2521942     -7.5234826     -7.5594736     -58.305867     -56.601233     -54.537783     -0.7563263     -0.68942681    -0.89444015     136.64507      136.61842      136.66703      99.860683      99.882098      99.86589       74.702368      74.723763      74.693042    
+     66000   1468.6429     -891.90582     -773.99786      2.2938491      1482.414       56.160228     -4.1318961     -7.2436172     -7.5080588     -7.5819411     -57.982694     -56.370777     -54.739699     -0.75092608    -0.69652428    -0.90242579     136.62154      136.60352      136.65359      99.85017       99.872559      99.849715      74.698926      74.716783      74.691294    
+     67500   1592.9841     -894.17166     -373.28608      2.2938491      1482.4608      66.22665      -4.1319088     -7.2020048     -7.5343208     -7.6502267     -57.737091     -56.058804     -54.410576     -0.74973866    -0.71379313    -0.92874192     136.61811      136.60579      136.64811      99.851858      99.868577      99.85379       74.695471      74.703568      74.688361    
+     69000   1451.6708     -892.24332     -42.454938      2.2938491      1482.3952      64.462379     -4.1318409     -7.2084429     -7.5095889     -7.6621307     -58.007656     -55.977537     -54.39909      -0.74311576    -0.67139652    -0.91195038     136.63393      136.60861      136.63564      99.845601      99.865271      99.865085      74.704656      74.707684      74.682318    
+     70500   1541.8751     -890.84273      603.87446      2.2938491      1482.1352      69.651346     -4.1319184     -7.1867148     -7.4795063     -7.6774435     -57.597661     -55.972955     -54.365809     -0.72507444    -0.63500349    -0.909513       136.63512      136.60177      136.63362      99.845987      99.867527      99.865623      74.698143      74.701585      74.674848    
+     72000   1469.8975     -890.17779     -712.95338      2.2938491      1482.2905      73.091503     -4.1319489     -7.1766057     -7.4591194     -7.660856      -57.657616     -55.981892     -54.095734     -0.71782602    -0.61875736    -0.91469335     136.63573      136.60382      136.63383      99.845901      99.869082      99.866108      74.699376      74.701787      74.672946    
+     73500   1571.7762     -894.46891      1835.3759      2.2938491      1482.42        84.062922     -4.1319557     -7.2310516     -7.4816168     -7.6691216     -57.820079     -55.90879      -54.134789     -0.73871067    -0.64971193    -0.93750027     136.63865      136.60893      136.64184      99.848872      99.876734      99.869374      74.696526      74.703769      74.671271    
+     75000   1668.0665     -889.10379      319.58734      2.2938491      1482.5795      91.590228     -4.1319353     -7.2136142     -7.4546526     -7.6863632     -57.99287      -55.973671     -54.462176     -0.7272861     -0.64541622    -0.9505418      136.64301      136.61457      136.65062      99.855439      99.877747      99.869599      74.701819      74.706548      74.682155    
+     76500   1660.1105     -891.61038      2128.1078      2.2938491      1482.4578      91.208675     -4.1318581     -7.2797412     -7.5002006     -7.6971338     -58.256724     -55.882133     -54.72244      -0.74105804    -0.65844257    -0.98078027     136.64403      136.6142       136.65487      99.855009      99.878188      99.868938      74.703354      74.70937       74.68632     
+     78000   1551.7441     -890.77214     -121.70935      2.2938491      1482.3519      85.597023     -4.1317377     -7.2689985     -7.4957494     -7.7185745     -58.313372     -56.092493     -54.841116     -0.75183521    -0.65377647    -0.97014055     136.62932      136.61045      136.63974      99.849688      99.867005      99.861641      74.698504      74.705574      74.688265    
+     79500   1451.11       -892.82037     -632.95505      2.2938491      1482.3476      87.575027     -4.1317651     -7.2403953     -7.4775336     -7.6689122     -58.32666      -56.035227     -54.817357     -0.72487208    -0.63508667    -0.96802939     136.62952      136.60836      136.63433      99.846727      99.865255      99.865022      74.698105      74.698515      74.685562    
+     81000   1497.4722     -891.00907     -173.43837      2.2938491      1482.3832      86.788447     -4.1317009     -7.270206      -7.4485143     -7.6702474     -58.081079     -55.896158     -54.762508     -0.72740498    -0.65433219    -0.95969011     136.62378      136.60331      136.63421      99.844906      99.86253       99.858317      74.695022      74.698559      74.689157    
+     82500   1555.7129     -892.58366      1904.2361      2.2938491      1482.3558      93.090261     -4.1317057     -7.2690799     -7.4631718     -7.7113864     -58.043005     -56.089191     -54.702244     -0.74777178    -0.68581389    -1.0039008      136.62292      136.59848      136.6349       99.844402      99.867354      99.856268      74.688752      74.699686      74.686532    
+     84000   1567.5762     -893.4426       1395.2965      2.2938491      1482.5162      94.678844     -4.1316985     -7.2414617     -7.4514971     -7.7059415     -57.823672     -56.159106     -54.697355     -0.73591992    -0.67263169    -0.99293636     136.62485      136.60365      136.63538      99.84546       99.868588      99.859502      74.694287      74.699557      74.688432    
+     85500   1432.2278     -889.0106      -1377.5411      2.2938491      1482.3155      93.438709     -4.1317406     -7.2231164     -7.4908049     -7.7049396     -57.502557     -56.145262     -54.63067      -0.75954036    -0.65582508    -1.0183515      136.6309       136.61047      136.64107      99.849588      99.871028      99.864254      74.699439      74.70335       74.691002    
+     87000   1460.2447     -891.89246     -0.80016568     2.2938491      1482.3382      88.386804     -4.1316936     -7.2264011     -7.5056543     -7.709398      -57.406671     -55.971898     -54.886302     -0.74942793    -0.65651161    -1.0146109      136.6237       136.59887      136.63315      99.842443      99.867697      99.856739      74.697165      74.70443       74.683402    
+     88500   1440.2891     -893.33008      524.68194      2.2938491      1482.3143      88.757788     -4.1317107     -7.2539574     -7.5019633     -7.6970553     -57.100672     -56.001078     -54.967854     -0.72231568    -0.67329128    -1.0062405      136.62754      136.60076      136.63746      99.841603      99.871714      99.857299      74.700219      74.708928      74.688224    
+     90000   1516.1386     -896.83736      514.25183      2.2938491      1482.4324      93.624187     -4.1316721     -7.2661783     -7.4872817     -7.6621711     -57.153939     -55.675044     -55.038702     -0.71162973    -0.65640585    -0.9901763      136.62634      136.5973       136.63636      99.840724      99.872434      99.853565      74.696616      74.71085       74.68682     
+     91500   1607.5754     -891.45362     -335.12175      2.2938491      1482.3634      96.295552     -4.1317168     -7.2512482     -7.4855921     -7.6563828     -57.333312     -55.871451     -54.885579     -0.71855253    -0.66451595    -0.9784755      136.62406      136.60485      136.63801      99.845387      99.869057      99.856498      74.69518       74.707799      74.689867    
+     93000   1460.9577     -891.0447       1910.5719      2.2938491      1482.5495      95.612581     -4.1316835     -7.2345819     -7.4872574     -7.6900538     -57.577838     -55.778305     -55.190243     -0.72452799    -0.67622846    -0.95134216     136.6155       136.58928      136.6336       99.838615      99.867719      99.849452      74.687208      74.706541      74.685971    
+     94500   1470.6227     -892.26051      270.39634      2.2938491      1482.5672      94.112066     -4.1317045     -7.2341279     -7.4928727     -7.6545536     -57.426957     -56.064962     -55.047123     -0.70451968    -0.67591615    -0.92282964     136.61646      136.59089      136.64185      99.840845      99.870383      99.849979      74.688749      74.709584      74.686957    
+     96000   1761.7597     -889.19794      2653.3494      2.2938491      1482.3672      85.211301     -4.1316762     -7.2539691     -7.4631657     -7.6913375     -57.327731     -55.963801     -55.013515     -0.71090453    -0.69574107    -0.92155635     136.60972      136.58428      136.62883      99.832904      99.864366      99.847749      74.688857      74.708236      74.682281    
+     97500   1481.5876     -894.20788     -389.53494      2.2938491      1482.2533      89.07951      -4.1317073     -7.25095       -7.4753287     -7.6606804     -57.47475      -56.096252     -55.158143     -0.71560129    -0.68873446    -0.93406162     136.61564      136.58736      136.63462      99.838049      99.868876      99.848771      74.686838      74.711562      74.683471    
+     99000   1495.5155     -891.01063      1680.8863      2.2938491      1482.2267      97.208165     -4.1317016     -7.277595      -7.5192558     -7.6344538     -57.476542     -56.383856     -54.882305     -0.74400485    -0.68726404    -0.94799728     136.61907      136.59346      136.63796      99.842727      99.870409      99.853088      74.685523      74.708843      74.684813    
+    100500   1467.1581     -889.95317      242.60103      2.2938491      1481.9829      97.224982     -4.1317571     -7.252584      -7.5076801     -7.6611416     -57.552637     -56.14004      -55.018801     -0.75385025    -0.69209438    -0.94398412     136.6207       136.60141      136.63777      99.846229      99.86929       99.857689      74.69078       74.705759      74.687925    
+    102000   1613.876      -891.23745      1375.2231      2.2938491      1481.8918      94.379877     -4.1317123     -7.2522696     -7.490171      -7.6514314     -57.635642     -55.888914     -54.994388     -0.75241502    -0.68960669    -0.91645246     136.62344      136.60488      136.63347      99.847338      99.865247      99.856123      74.695679      74.707583      74.693448    
+    103500   1366.8885     -892.68641     -434.73129      2.2938491      1481.866       97.233875     -4.1317222     -7.2341862     -7.4693846     -7.6427203     -57.848484     -55.98048      -55.261348     -0.74622204    -0.68309934    -0.92443719     136.62181      136.61267      136.63941      99.856541      99.863371      99.859527      74.696212      74.702525      74.694062    
+    105000   1566.8173     -889.64302      52.134848      2.2938491      1481.9555      94.617908     -4.131708      -7.2078092     -7.490984      -7.6511905     -57.877166     -55.970863     -55.392031     -0.74617361    -0.69517832    -0.94219586     136.62317      136.61282      136.63557      99.853702      99.862156      99.858588      74.697837      74.703415      74.693222    
+    106500   1510.7795     -891.83105      912.04973      2.2938491      1481.9273      94.050693     -4.1317245     -7.2274362     -7.4958029     -7.6473799     -57.9481       -55.855934     -55.405593     -0.7612426     -0.70193323    -0.94170435     136.61865      136.60991      136.63015      99.851136      99.858763      99.857942      74.697833      74.700173      74.690954    
+    108000   1455.2205     -886.40658      557.80643      2.2938491      1481.8672      90.932719     -4.131639      -7.2156616     -7.5140992     -7.6592343     -57.875096     -56.121921     -55.441901     -0.77520355    -0.7082224     -0.95332709     136.61521      136.60854      136.62307      99.844819      99.853589      99.857619      74.706032      74.702008      74.690719    
+    109500   1591.694      -890.12115      2111.7582      2.2938491      1481.9081      90.818335     -4.1316826     -7.2099875     -7.5036851     -7.6146732     -57.901962     -56.080481     -55.335907     -0.77541222    -0.70215363    -0.94640585     136.62449      136.62284      136.63316      99.852345      99.858242      99.864241      74.712062      74.706711      74.695773    
+    111000   1401.5464     -889.70209     -1162.998       2.2938491      1481.8995      90.785361     -4.1317103     -7.2232569     -7.4975842     -7.6122167     -57.814589     -56.145176     -55.237091     -0.77101386    -0.71297505    -0.93787376     136.62319      136.62624      136.63278      99.855678      99.855147      99.865946      74.710261      74.703628      74.698218    
+    112500   1661.4542     -893.40947      3577.1279      2.2938491      1482.0712      91.936529     -4.1316922     -7.2363752     -7.490673      -7.6041227     -57.793279     -56.031961     -55.425678     -0.76646862    -0.71410904    -0.9310629      136.61332      136.62225      136.62704      99.856804      99.84979       99.862862      74.707371      74.696176      74.697236    
+    114000   1547.0639     -887.44417      1477.9344      2.2938491      1482.0257      92.747503     -4.131727      -7.2300662     -7.4797162     -7.5970492     -57.853023     -55.961882     -55.370161     -0.75229192    -0.6895434     -0.93030859     136.61656      136.62515      136.62686      99.855862      99.853722      99.86337       74.71008       74.698813      74.695278    
+    115500   1439.5189     -890.25524      1449.2504      2.2938491      1482.1027      93.092922     -4.1317311     -7.2248464     -7.4844791     -7.577668      -57.724672     -55.908203     -55.477058     -0.75703148    -0.69213445    -0.93063769     136.61287      136.62652      136.63064      99.861066      99.855191      99.860674      74.707263      74.699878      74.698782    
+    117000   1484.5557     -888.52105      62.875599      2.2938491      1481.939       88.920925     -4.1316902     -7.2401277     -7.4688263     -7.5738313     -57.623793     -55.827804     -55.470646     -0.7670686     -0.70720567    -0.94065827     136.61043      136.62028      136.62637      99.856362      99.852679      99.856577      74.7054        74.702523      74.700062    
+    118500   1544.5557     -897.27305      290.28551      2.2938491      1482.0321      82.378509     -4.1316258     -7.2550568     -7.4962409     -7.6069951     -57.791253     -55.82989      -55.246167     -0.7749151     -0.72530054    -0.96204389     136.60394      136.61474      136.6218       99.851596      99.848741      99.849294      74.707077      74.705425      74.700726    
+    120000   1478.3947     -892.7268      -577.38167      2.2938491      1481.8729      84.389547     -4.1316655     -7.2406756     -7.4760807     -7.571379      -57.99213      -55.95264      -55.45397      -0.77057679    -0.71238268    -0.94097166     136.60946      136.62355      136.62508      99.855739      99.849821      99.856483      74.708864      74.703347      74.704105    
+    121500   1529.2571     -890.35258      214.27253      2.2938491      1481.8862      79.172239     -4.131618      -7.2321448     -7.4640098     -7.5859318     -57.999026     -55.743602     -55.374383     -0.76556556    -0.72763717    -0.94266473     136.60096      136.62176      136.61876      99.853547      99.843769      99.850416      74.711419      74.702896      74.703593    
+    123000   1592.6338     -895.89179      1618.5405      2.2938491      1481.8996      82.460382     -4.1316142     -7.2304535     -7.4384951     -7.5700086     -57.853634     -55.668494     -55.236154     -0.75305506    -0.73385059    -0.93874018     136.59877      136.61927      136.61316      99.852817      99.840785      99.851696      74.710721      74.698867      74.700648    
+    124500   1481.1564     -896.96342      324.3934       2.2938491      1481.8895      85.319881     -4.1316244     -7.2264693     -7.4227219     -7.5551714     -57.777484     -55.785962     -55.26024      -0.75234123    -0.73009637    -0.93269204     136.59932      136.61758      136.61173      99.852222      99.841031      99.851213      74.709885      74.698336      74.698938    
+    126000   1366.1089     -891.93997     -658.32428      2.2938491      1481.7226      78.355779     -4.1316207     -7.2488328     -7.4329154     -7.5647275     -57.916784     -55.857672     -55.218103     -0.76146388    -0.73488986    -0.92639796     136.5948       136.61742      136.60582      99.851304      99.835211      99.848225      74.709524      74.694785      74.702522    
+    127500   1505.7295     -893.82427      1963.9643      2.2938491      1481.8782      87.640052     -4.1316687     -7.277167      -7.4400402     -7.5639761     -57.931692     -55.857053     -55.327085     -0.77752365    -0.7559997     -0.93064472     136.60295      136.6295       136.61443      99.859242      99.841072      99.856065      74.711211      74.693396      74.703574    
+    129000   1544.571      -892.03159     -527.07176      2.2938491      1482.0193      87.794364     -4.1316821     -7.2698344     -7.4346091     -7.5684319     -57.869829     -55.877329     -55.269055     -0.77585053    -0.73210247    -0.92680166     136.60317      136.63098      136.61634      99.86071       99.839607      99.856208      74.712198      74.695158      74.705047    
+    130500   1563.3858     -889.50411     -87.198132      2.2938491      1482.0526      81.485975     -4.1316493     -7.2663101     -7.4269998     -7.5691984     -57.836151     -55.897446     -55.110745     -0.7681867     -0.72744291    -0.91874044     136.59693      136.63004      136.61117      99.858337      99.836672      99.849979      74.711563      74.695134      74.708137    
+    132000   1553.6055     -896.15176      740.11093      2.2938491      1481.9674      80.783301     -4.1316735     -7.2824836     -7.4350446     -7.5489937     -57.950565     -55.829897     -55.147418     -0.79446196    -0.73309725    -0.92126843     136.59425      136.62943      136.61481      99.860995      99.838059      99.848436      74.708412      74.695423      74.708926    
+    133500   1385.0177     -892.27993     -907.20247      2.2938491      1481.8295      79.187393     -4.1316431     -7.2781202     -7.4600968     -7.5283409     -58.068566     -55.837667     -54.995174     -0.79075959    -0.72422066    -0.92463565     136.58806      136.62239      136.6053       99.858416      99.830029      99.847215      74.70793       74.690917      74.708181    
+    135000   1483.9097     -893.96772     -2166.9672      2.2938491      1481.8458      79.724142     -4.1316572     -7.2532514     -7.4529684     -7.5151627     -58.117754     -55.762813     -55.044672     -0.78734824    -0.71937479    -0.9191986      136.5908       136.62612      136.60205      99.856567      99.829771      99.850178      74.711435      74.688994      74.708456    
+    136500   1600.2522     -890.70516      609.13895      2.2938491      1481.92        83.006512     -4.1316674     -7.258606      -7.4315875     -7.5020899     -58.1938       -55.794999     -54.94864      -0.77941653    -0.72340994    -0.90867059     136.5924       136.62407      136.6027       99.858372      99.830876      99.850851      74.70873       74.687502      74.705977    
+    138000   1502.6753     -890.61112      391.94407      2.2938491      1482.0167      76.016016     -4.1316051     -7.2681189     -7.4332901     -7.5246594     -58.549025     -55.68375      -55.083251     -0.7721303     -0.73534454    -0.91398112     136.5902       136.61295      136.59058      99.848968      99.826477      99.845811      74.7088        74.685769      74.700689    
+    139500   1356.6079     -892.88412      443.66566      2.2938491      1482.1012      75.175931     -4.1315823     -7.272648      -7.4202164     -7.5435138     -58.430256     -55.645142     -55.177498     -0.77281637    -0.74277362    -0.90655462     136.58594      136.60941      136.58868      99.8471        99.825215      99.844524      74.704379      74.684246      74.698048    
+    141000   1536.8299     -891.3964       1488.9232      2.2938491      1482.1777      70.161617     -4.1315549     -7.2870883     -7.4331937     -7.5306099     -58.52421      -55.722214     -55.042544     -0.74933771    -0.74261337    -0.87760623     136.58324      136.61276      136.58989      99.849169      99.823054      99.843296      74.706773      74.681129      74.703048    
+    142500   1436.4404     -893.92271      574.36968      2.2938491      1482.0701      72.237377     -4.1316031     -7.2838066     -7.4093453     -7.5146661     -58.526669     -55.658527     -54.961371     -0.75069722    -0.74058553    -0.87613316     136.58937      136.61441      136.59146      99.848728      99.827923      99.846928      74.706061      74.681733      74.697755    
+    144000   1489.9179     -891.89057      874.84954      2.2938491      1482.1193      76.069588     -4.1316094     -7.2964678     -7.3973197     -7.5029947     -58.56494      -55.90659      -54.948484     -0.74022244    -0.75134582    -0.87359031     136.59283      136.61825      136.59298      99.85297       99.828592      99.848855      74.708201      74.681372      74.698936    
+    145500   1498.8873     -892.88995     -375.19001      2.2938491      1482.1293      78.637484     -4.1316333     -7.28757       -7.3758785     -7.5097553     -58.819672     -55.915661     -54.947745     -0.73771147    -0.76005783    -0.87268243     136.59805      136.62289      136.59468      99.853239      99.831254      99.853326      74.712898      74.684719      74.697923    
+    147000   1522.292      -888.44727      1193.3345      2.2938491      1482.274       82.096416     -4.1316355     -7.2628288     -7.3837513     -7.5079984     -58.864236     -55.949971     -55.052575     -0.72231418    -0.74804745    -0.87292368     136.60062      136.62844      136.59425      99.855419      99.831528      99.855082      74.715145      74.682637      74.701191    
+    148500   1570.9693     -893.72505      672.43585      2.2938491      1482.3953      88.359724     -4.1316418     -7.2884009     -7.3644359     -7.5112899     -58.807712     -55.988036     -55.099847     -0.72835513    -0.74530355    -0.87637008     136.60096      136.6326       136.59779      99.857791      99.834031      99.857841      74.715094      74.683359      74.70131     
+    150000   1449.0081     -891.81638     -714.54867      2.2938491      1482.3667      90.591195     -4.1316589     -7.3037214     -7.3497793     -7.5219215     -58.757005     -56.00609      -55.081797     -0.72611841    -0.75187625    -0.87207291     136.60564      136.63782      136.59487      99.857615      99.835445      99.86176       74.718484      74.683132      74.699142    
+Loop time of 18.3423 on 4 procs for 150000 steps with 216 atoms
+
+Performance: 541.227 ns/day, 0.044 hours/ns, 8177.811 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 12.192     | 12.302     | 12.366     |   2.0 | 67.07
+Neigh   | 0.16441    | 0.16492    | 0.16576    |   0.1 |  0.90
+Comm    | 2.4159     | 2.4795     | 2.5866     |   4.3 | 13.52
+Output  | 0.0030494  | 0.0033533  | 0.0042086  |   0.9 |  0.02
+Modify  | 3.1243     | 3.1322     | 3.1398     |   0.3 | 17.08
+Other   |            | 0.2608     |            |       |  1.42
+
+Nlocal:             54 ave          54 max          54 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:         334.75 ave         338 max         331 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:       1426.5 ave        1439 max        1408 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+
+Total # of neighbors = 5706
+Ave neighs/atom = 26.416667
+Neighbor list builds = 2567
+Dangerous builds = 0
+
+# Output final values
+
+include final_output.in
+# Average moduli for cubic crystals
+
+variable C11cubic equal (${C11}+${C22}+${C33})/3.0
+variable C11cubic equal (133.317541070292+${C22}+${C33})/3.0
+variable C11cubic equal (133.317541070292+133.303658933287+${C33})/3.0
+variable C11cubic equal (133.317541070292+133.303658933287+133.088561493082)/3.0
+variable C12cubic equal (${C12}+${C13}+${C23})/3.0
+variable C12cubic equal (73.9923654361203+${C13}+${C23})/3.0
+variable C12cubic equal (73.9923654361203+73.9312552589804+${C23})/3.0
+variable C12cubic equal (73.9923654361203+73.9312552589804+73.8270687089798)/3.0
+variable C44cubic equal (${C44}+${C55}+${C66})/3.0
+variable C44cubic equal (43.1084188147025+${C55}+${C66})/3.0
+variable C44cubic equal (43.1084188147025+45.8371646999798+${C66})/3.0
+variable C44cubic equal (43.1084188147025+45.8371646999798+46.7877718062386)/3.0
+
+variable bulkmodulus equal (${C11cubic}+2*${C12cubic})/3.0
+variable bulkmodulus equal (133.236587165554+2*${C12cubic})/3.0
+variable bulkmodulus equal (133.236587165554+2*73.9168964680268)/3.0
+variable shearmodulus1 equal ${C44cubic}
+variable shearmodulus1 equal 45.2444517736403
+variable shearmodulus2 equal (${C11cubic}-${C12cubic})/2.0
+variable shearmodulus2 equal (133.236587165554-${C12cubic})/2.0
+variable shearmodulus2 equal (133.236587165554-73.9168964680268)/2.0
+variable poissonratio equal 1.0/(1.0+${C11cubic}/${C12cubic})
+variable poissonratio equal 1.0/(1.0+133.236587165554/${C12cubic})
+variable poissonratio equal 1.0/(1.0+133.236587165554/73.9168964680268)
+
+# For Stillinger-Weber silicon, the analytical results
+# are known to be (E. R. Cowley, 1988):
+#               C11 = 151.4 GPa
+#               C12 = 76.4 GPa
+#               C44 = 56.4 GPa
+
+#print "========================================="
+#print "Components of the Elastic Constant Tensor"
+#print "========================================="
+
+print "Elastic Constant C11 = ${C11} ${cunits}"
+Elastic Constant C11 = 133.317541070292 GPa
+print "Elastic Constant C22 = ${C22} ${cunits}"
+Elastic Constant C22 = 133.303658933287 GPa
+print "Elastic Constant C33 = ${C33} ${cunits}"
+Elastic Constant C33 = 133.088561493082 GPa
+
+print "Elastic Constant C12 = ${C12} ${cunits}"
+Elastic Constant C12 = 73.9923654361203 GPa
+print "Elastic Constant C13 = ${C13} ${cunits}"
+Elastic Constant C13 = 73.9312552589804 GPa
+print "Elastic Constant C23 = ${C23} ${cunits}"
+Elastic Constant C23 = 73.8270687089798 GPa
+
+print "Elastic Constant C44 = ${C44} ${cunits}"
+Elastic Constant C44 = 43.1084188147025 GPa
+print "Elastic Constant C55 = ${C55} ${cunits}"
+Elastic Constant C55 = 45.8371646999798 GPa
+print "Elastic Constant C66 = ${C66} ${cunits}"
+Elastic Constant C66 = 46.7877718062386 GPa
+
+print "Elastic Constant C14 = ${C14} ${cunits}"
+Elastic Constant C14 = 0.0767019895461112 GPa
+print "Elastic Constant C15 = ${C15} ${cunits}"
+Elastic Constant C15 = 0.160081312432549 GPa
+print "Elastic Constant C16 = ${C16} ${cunits}"
+Elastic Constant C16 = -0.0672322473606912 GPa
+
+print "Elastic Constant C24 = ${C24} ${cunits}"
+Elastic Constant C24 = -0.0980703737031021 GPa
+print "Elastic Constant C25 = ${C25} ${cunits}"
+Elastic Constant C25 = 0.425094496914652 GPa
+print "Elastic Constant C26 = ${C26} ${cunits}"
+Elastic Constant C26 = -0.061665192022258 GPa
+
+print "Elastic Constant C34 = ${C34} ${cunits}"
+Elastic Constant C34 = -0.0939770954478323 GPa
+print "Elastic Constant C35 = ${C35} ${cunits}"
+Elastic Constant C35 = 0.10019558502976 GPa
+print "Elastic Constant C36 = ${C36} ${cunits}"
+Elastic Constant C36 = 0.246165012383149 GPa
+
+print "Elastic Constant C45 = ${C45} ${cunits}"
+Elastic Constant C45 = 0.451034755300606 GPa
+print "Elastic Constant C46 = ${C46} ${cunits}"
+Elastic Constant C46 = 0.53971304682664 GPa
+print "Elastic Constant C56 = ${C56} ${cunits}"
+Elastic Constant C56 = -0.243078648160722 GPa
+
+print "========================================="
+=========================================
+print "Average properties for a cubic crystal"
+Average properties for a cubic crystal
+print "========================================="
+=========================================
+
+print "Bulk Modulus = ${bulkmodulus} ${cunits}"
+Bulk Modulus = 93.6901267005359 GPa
+print "Shear Modulus 1 = ${shearmodulus1} ${cunits}"
+Shear Modulus 1 = 45.2444517736403 GPa
+print "Shear Modulus 2 = ${shearmodulus2} ${cunits}"
+Shear Modulus 2 = 29.6598453487636 GPa
+print "Poisson Ratio = ${poissonratio}"
+Poisson Ratio = 0.356821884775895
+
+# summarize sampling protocol
+
+variable tmp equal atoms
+print "Number of atoms = ${tmp}"
+Number of atoms = 216
+print "Stress sampling interval = ${nevery}"
+Stress sampling interval = 10
+variable tmp equal ${nrun}/${nevery}
+variable tmp equal 150000/${nevery}
+variable tmp equal 150000/10
+print "Stress sample count = ${tmp}"
+Stress sample count = 15000
+print "Born sampling interval = ${neveryborn}"
+Born sampling interval = 100
+variable tmp equal ${nrun}/${neveryborn}
+variable tmp equal 150000/${neveryborn}
+variable tmp equal 150000/100
+print "Born sample count = ${tmp}"
+Born sample count = 1500
+Total wall time: 0:00:19

examples/ELASTIC_T/BORN_MATRIX/Silicon/log.16May22.tri.g++.4

@@ -0,0 +1,662 @@
+
+# select temperature and pressure (lattice constant)
+
+variable temp index 1477.0                 # temperature of initial sample
+variable a index 5.457                     # lattice constant
+
+# select sampling parameters, important for speed/convergence
+
+variable nthermo index 1500               # interval for thermo output
+variable nevery index 10                  # stress sampling interval
+variable neveryborn index 100             # Born sampling interval
+variable timestep index 0.000766          # timestep
+variable nlat index 3                     # number of lattice unit cells
+
+# other settings
+
+variable mass1 index 28.06                # mass
+variable tdamp index 0.01                 # time constant for thermostat
+variable seed index 123457                # seed for thermostat
+variable thermostat index 1               # 0 if NVE, 1 if NVT
+variable delta index 1.0e-6               # Born numdiff strain magnitude
+
+# hard-coded rules-of-thumb for run length, etc.
+
+variable nfreq equal ${nthermo}           # interval for averaging output
+variable nfreq equal 1500           
+variable nrepeat equal floor(${nfreq}/${nevery}) # number of samples
+variable nrepeat equal floor(1500/${nevery}) 
+variable nrepeat equal floor(1500/10) 
+variable nrepeatborn equal floor(${nfreq}/${neveryborn}) # number of samples
+variable nrepeatborn equal floor(1500/${neveryborn}) 
+variable nrepeatborn equal floor(1500/100) 
+variable nequil equal 10*${nthermo}       # length of equilibration run
+variable nequil equal 10*1500       
+variable nrun equal 100*${nthermo}        # length of equilibrated run
+variable nrun equal 100*1500        
+
+# this generates a general triclinic cell
+# conforming to LAMMPS cell (upper triangular)
+
+units		metal
+box 		tilt large
+
+# unit lattice vectors are
+# a1 = (a1x 0 0)
+# a2 = (a2x a2y 0)
+# a3 = (a3x a3y a3z)
+
+variable        a1x index 1
+variable 	a2x index 0
+variable 	a2y index 1
+variable 	a3x index 0
+variable 	a3y index 0
+variable	a3z index 1
+variable	atmp equal $a
+variable	atmp equal 5.457
+variable 	l index $a
+variable 	l index 5.457
+variable	basis index "basis 0    0    0  basis 0.25 0.25 0.25 basis 0    0.5  0.5 basis 0.25 0.75 0.75 basis 0.5  0    0.5 basis 0.75 0.25 0.75 basis 0.5  0.5  0 basis 0.75 0.75 0.25"
+lattice         custom ${l}                             a1 ${a1x}      0      0                 a2 ${a2x} ${a2y}      0                 a3 ${a3x} ${a3y} ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 3.8586817049349893                             a1 ${a1x}      0      0                 a2 ${a2x} ${a2y}      0                 a3 ${a3x} ${a3y} ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 3.8586817049349893                             a1 1.0      0      0                 a2 ${a2x} ${a2y}      0                 a3 ${a3x} ${a3y} ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 3.8586817049349893                             a1 1.0      0      0                 a2 0.4999999999999999 ${a2y}      0                 a3 ${a3x} ${a3y} ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 3.8586817049349893                             a1 1.0      0      0                 a2 0.4999999999999999 0.8660254037844385      0                 a3 ${a3x} ${a3y} ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 3.8586817049349893                             a1 1.0      0      0                 a2 0.4999999999999999 0.8660254037844385      0                 a3 0.5 ${a3y} ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 3.8586817049349893                             a1 1.0      0      0                 a2 0.4999999999999999 0.8660254037844385      0                 a3 0.5 0.2886751345948129 ${a3z}                 ${basis}    		spacing 1 1 1
+lattice         custom 3.8586817049349893                             a1 1.0      0      0                 a2 0.4999999999999999 0.8660254037844385      0                 a3 0.5 0.2886751345948129 0.8164965809277259                 ${basis}    		spacing 1 1 1
+lattice         custom 3.8586817049349893                             a1 1.0      0      0                 a2 0.4999999999999999 0.8660254037844385      0                 a3 0.5 0.2886751345948129 0.8164965809277259                 basis 0 0 0 basis 0.25 0.25 0.25     		spacing 1 1 1
+Lattice spacing in x,y,z = 3.8586817 3.8586817 3.8586817
+
+region		box prism 0 ${a1x} 0 ${a2y} 0 ${a3z} ${a2x} ${a3x} ${a3y}
+region		box prism 0 1.0 0 ${a2y} 0 ${a3z} ${a2x} ${a3x} ${a3y}
+region		box prism 0 1.0 0 0.8660254037844385 0 ${a3z} ${a2x} ${a3x} ${a3y}
+region		box prism 0 1.0 0 0.8660254037844385 0 0.8164965809277259 ${a2x} ${a3x} ${a3y}
+region		box prism 0 1.0 0 0.8660254037844385 0 0.8164965809277259 0.4999999999999999 ${a3x} ${a3y}
+region		box prism 0 1.0 0 0.8660254037844385 0 0.8164965809277259 0.4999999999999999 0.5 ${a3y}
+region		box prism 0 1.0 0 0.8660254037844385 0 0.8164965809277259 0.4999999999999999 0.5 0.2886751345948129
+
+create_box	1 box
+Created triclinic box = (0 0 0) to (3.8586817 3.3417164 3.1506004) with tilt (1.9293409 1.9293409 1.1139055)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 2 atoms
+  using lattice units in triclinic box = (0 0 0) to (3.8586817 3.3417164 3.1506004) with tilt (1.9293409 1.9293409 1.1139055)
+  create_atoms CPU = 0.000 seconds
+mass 1 ${mass1}
+mass 1 28.06
+replicate ${nlat} ${nlat} ${nlat}
+replicate 5 ${nlat} ${nlat}
+replicate 5 5 ${nlat}
+replicate 5 5 5
+Replicating atoms ...
+  triclinic box = (0 0 0) to (19.293409 16.708582 15.753002) with tilt (9.6467043 9.6467043 5.5695273)
+  2 by 1 by 2 MPI processor grid
+  250 atoms
+  replicate CPU = 0.000 seconds
+velocity	all create ${temp} 87287
+velocity	all create 1477.0 87287
+
+
+
+# Compute initial state
+
+include potential.in
+# NOTE: This script can be modified for different pair styles
+# See in.elastic for more info.
+
+reset_timestep 0
+
+# Choose potential
+pair_style	sw
+pair_coeff * * Si.sw Si
+Reading sw potential file Si.sw with DATE: 2007-06-11
+
+# Setup neighbor style
+neighbor 1.0 nsq
+neigh_modify once no every 1 delay 0 check yes
+
+# Setup MD
+
+timestep ${timestep}
+timestep 0.000766
+fix 4 all nve
+if "${thermostat} == 1" then    "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}
+fix 5 all langevin 1477.0 ${temp} ${tdamp} ${seed}
+fix 5 all langevin 1477.0 1477.0 ${tdamp} ${seed}
+fix 5 all langevin 1477.0 1477.0 0.01 ${seed}
+fix 5 all langevin 1477.0 1477.0 0.01 123457
+
+
+thermo_style custom step temp pe press density
+run ${nequil}
+run 15000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.77118
+  ghost atom cutoff = 4.77118
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sw, perpetual
+      attributes: full, newton on
+      pair build: full/nsq
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.058 | 3.058 | 3.059 Mbytes
+   Step          Temp          PotEng         Press         Density    
+         0   1477          -1083.8249     -4258.3947      2.2938491    
+     15000   1496.4515     -1030.8279      1702.5821      2.2938491    
+Loop time of 1.93162 on 4 procs for 15000 steps with 250 atoms
+
+Performance: 513.941 ns/day, 0.047 hours/ns, 7765.521 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.233      | 1.4215     | 1.6958     |  14.2 | 73.59
+Neigh   | 0.020173   | 0.022348   | 0.025604   |   1.3 |  1.16
+Comm    | 0.15771    | 0.43281    | 0.62056    |  25.8 | 22.41
+Output  | 1.2841e-05 | 1.4604e-05 | 1.9543e-05 |   0.0 |  0.00
+Modify  | 0.021536   | 0.025134   | 0.030087   |   2.0 |  1.30
+Other   |            | 0.02978    |            |       |  1.54
+
+Nlocal:           62.5 ave          74 max          58 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost:          429.5 ave         465 max         391 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:       1649.5 ave        1943 max        1526 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 6598
+Ave neighs/atom = 26.392
+Neighbor list builds = 261
+Dangerous builds = 0
+
+# Run dynamics
+
+include potential.in
+# NOTE: This script can be modified for different pair styles
+# See in.elastic for more info.
+
+reset_timestep 0
+
+# Choose potential
+pair_style	sw
+pair_coeff * * Si.sw Si
+Reading sw potential file Si.sw with DATE: 2007-06-11
+
+# Setup neighbor style
+neighbor 1.0 nsq
+neigh_modify once no every 1 delay 0 check yes
+
+# Setup MD
+
+timestep ${timestep}
+timestep 0.000766
+fix 4 all nve
+if "${thermostat} == 1" then    "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
+fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}
+fix 5 all langevin 1477.0 ${temp} ${tdamp} ${seed}
+fix 5 all langevin 1477.0 1477.0 ${tdamp} ${seed}
+fix 5 all langevin 1477.0 1477.0 0.01 ${seed}
+fix 5 all langevin 1477.0 1477.0 0.01 123457
+
+
+include output.in
+# Setup output
+
+# Stress fluctuation term F
+
+compute stress all pressure thermo_temp
+variable s1 equal c_stress[1]
+variable s2 equal c_stress[2]
+variable s3 equal c_stress[3]
+variable s4 equal c_stress[6]
+variable s5 equal c_stress[5]
+variable s6 equal c_stress[4]
+
+variable s11 equal v_s1*v_s1
+variable s22 equal v_s2*v_s2
+variable s33 equal v_s3*v_s3
+variable s44 equal v_s4*v_s4
+variable s55 equal v_s5*v_s5
+variable s66 equal v_s6*v_s6
+variable s33 equal v_s3*v_s3
+variable s12 equal v_s1*v_s2
+variable s13 equal v_s1*v_s3
+variable s14 equal v_s1*v_s4
+variable s15 equal v_s1*v_s5
+variable s16 equal v_s1*v_s6
+variable s23 equal v_s2*v_s3
+variable s24 equal v_s2*v_s4
+variable s25 equal v_s2*v_s5
+variable s26 equal v_s2*v_s6
+variable s34 equal v_s3*v_s4
+variable s35 equal v_s3*v_s5
+variable s36 equal v_s3*v_s6
+variable s45 equal v_s4*v_s5
+variable s46 equal v_s4*v_s6
+variable s56 equal v_s5*v_s6
+
+variable mytemp equal temp
+variable mypress equal press
+variable mype equal pe/atoms
+fix avt all ave/time ${nevery} ${nrepeat} ${nfreq} v_mytemp ave running
+fix avt all ave/time 10 ${nrepeat} ${nfreq} v_mytemp ave running
+fix avt all ave/time 10 150 ${nfreq} v_mytemp ave running
+fix avt all ave/time 10 150 1500 v_mytemp ave running
+fix avp all ave/time ${nevery} ${nrepeat} ${nfreq} v_mypress ave running
+fix avp all ave/time 10 ${nrepeat} ${nfreq} v_mypress ave running
+fix avp all ave/time 10 150 ${nfreq} v_mypress ave running
+fix avp all ave/time 10 150 1500 v_mypress ave running
+fix avpe all ave/time ${nevery} ${nrepeat} ${nfreq} v_mype ave running
+fix avpe all ave/time 10 ${nrepeat} ${nfreq} v_mype ave running
+fix avpe all ave/time 10 150 ${nfreq} v_mype ave running
+fix avpe all ave/time 10 150 1500 v_mype ave running
+fix avs all ave/time ${nevery} ${nrepeat} ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
+fix avs all ave/time 10 ${nrepeat} ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
+fix avs all ave/time 10 150 ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
+fix avs all ave/time 10 150 1500 v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
+fix avssq all ave/time ${nevery} ${nrepeat} ${nfreq} v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
+fix avssq all ave/time 10 ${nrepeat} ${nfreq} v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
+fix avssq all ave/time 10 150 ${nfreq} v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
+fix avssq all ave/time 10 150 1500 v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
+
+# bar to GPa
+variable pconv equal 1.0e5/1.0e9
+variable cunits index GPa
+# metal unit constants from LAMMPS
+# force->nktv2p = 1.6021765e6;
+# force->boltz = 8.617343e-5;
+variable boltz equal 8.617343e-5
+variable nktv2p equal 1.6021765e6
+variable vkt equal vol/(${boltz}*${temp})/${nktv2p}
+variable vkt equal vol/(8.617343e-05*${temp})/${nktv2p}
+variable vkt equal vol/(8.617343e-05*1477.0)/${nktv2p}
+variable vkt equal vol/(8.617343e-05*1477.0)/1602176.5
+variable ffac equal ${pconv}*${vkt}
+variable ffac equal 0.0001*${vkt}
+variable ffac equal 0.0001*0.0249027696047235
+
+variable F11 equal -(f_avssq[1]-f_avs[1]*f_avs[1])*${ffac}
+variable F11 equal -(f_avssq[1]-f_avs[1]*f_avs[1])*2.49027696047235e-06
+variable F22 equal -(f_avssq[2]-f_avs[2]*f_avs[2])*${ffac}
+variable F22 equal -(f_avssq[2]-f_avs[2]*f_avs[2])*2.49027696047235e-06
+variable F33 equal -(f_avssq[3]-f_avs[3]*f_avs[3])*${ffac}
+variable F33 equal -(f_avssq[3]-f_avs[3]*f_avs[3])*2.49027696047235e-06
+variable F44 equal -(f_avssq[4]-f_avs[4]*f_avs[4])*${ffac}
+variable F44 equal -(f_avssq[4]-f_avs[4]*f_avs[4])*2.49027696047235e-06
+variable F55 equal -(f_avssq[5]-f_avs[5]*f_avs[5])*${ffac}
+variable F55 equal -(f_avssq[5]-f_avs[5]*f_avs[5])*2.49027696047235e-06
+variable F66 equal -(f_avssq[6]-f_avs[6]*f_avs[6])*${ffac}
+variable F66 equal -(f_avssq[6]-f_avs[6]*f_avs[6])*2.49027696047235e-06
+
+variable F12 equal -(f_avssq[7]-f_avs[1]*f_avs[2])*${ffac}
+variable F12 equal -(f_avssq[7]-f_avs[1]*f_avs[2])*2.49027696047235e-06
+variable F13 equal -(f_avssq[8]-f_avs[1]*f_avs[3])*${ffac}
+variable F13 equal -(f_avssq[8]-f_avs[1]*f_avs[3])*2.49027696047235e-06
+variable F14 equal -(f_avssq[9]-f_avs[1]*f_avs[4])*${ffac}
+variable F14 equal -(f_avssq[9]-f_avs[1]*f_avs[4])*2.49027696047235e-06
+variable F15 equal -(f_avssq[10]-f_avs[1]*f_avs[5])*${ffac}
+variable F15 equal -(f_avssq[10]-f_avs[1]*f_avs[5])*2.49027696047235e-06
+variable F16 equal -(f_avssq[11]-f_avs[1]*f_avs[6])*${ffac}
+variable F16 equal -(f_avssq[11]-f_avs[1]*f_avs[6])*2.49027696047235e-06
+
+variable F23 equal -(f_avssq[12]-f_avs[2]*f_avs[3])*${ffac}
+variable F23 equal -(f_avssq[12]-f_avs[2]*f_avs[3])*2.49027696047235e-06
+variable F24 equal -(f_avssq[13]-f_avs[2]*f_avs[4])*${ffac}
+variable F24 equal -(f_avssq[13]-f_avs[2]*f_avs[4])*2.49027696047235e-06
+variable F25 equal -(f_avssq[14]-f_avs[2]*f_avs[5])*${ffac}
+variable F25 equal -(f_avssq[14]-f_avs[2]*f_avs[5])*2.49027696047235e-06
+variable F26 equal -(f_avssq[15]-f_avs[2]*f_avs[6])*${ffac}
+variable F26 equal -(f_avssq[15]-f_avs[2]*f_avs[6])*2.49027696047235e-06
+
+variable F34 equal -(f_avssq[16]-f_avs[3]*f_avs[4])*${ffac}
+variable F34 equal -(f_avssq[16]-f_avs[3]*f_avs[4])*2.49027696047235e-06
+variable F35 equal -(f_avssq[17]-f_avs[3]*f_avs[5])*${ffac}
+variable F35 equal -(f_avssq[17]-f_avs[3]*f_avs[5])*2.49027696047235e-06
+variable F36 equal -(f_avssq[18]-f_avs[3]*f_avs[6])*${ffac}
+variable F36 equal -(f_avssq[18]-f_avs[3]*f_avs[6])*2.49027696047235e-06
+
+variable F45 equal -(f_avssq[19]-f_avs[4]*f_avs[5])*${ffac}
+variable F45 equal -(f_avssq[19]-f_avs[4]*f_avs[5])*2.49027696047235e-06
+variable F46 equal -(f_avssq[20]-f_avs[4]*f_avs[6])*${ffac}
+variable F46 equal -(f_avssq[20]-f_avs[4]*f_avs[6])*2.49027696047235e-06
+
+variable F56 equal -(f_avssq[21]-f_avs[5]*f_avs[6])*${ffac}
+variable F56 equal -(f_avssq[21]-f_avs[5]*f_avs[6])*2.49027696047235e-06
+
+# Born term
+
+compute     virial all pressure NULL virial
+compute     born all born/matrix numdiff ${delta} virial
+compute     born all born/matrix numdiff 1.0e-6 virial
+fix 	    avborn all ave/time ${neveryborn} ${nrepeatborn} ${nfreq} c_born[*] ave running
+fix 	    avborn all ave/time 100 ${nrepeatborn} ${nfreq} c_born[*] ave running
+fix 	    avborn all ave/time 100 15 ${nfreq} c_born[*] ave running
+fix 	    avborn all ave/time 100 15 1500 c_born[*] ave running
+
+variable bfac equal ${pconv}*${nktv2p}/vol
+variable bfac equal 0.0001*${nktv2p}/vol
+variable bfac equal 0.0001*1602176.5/vol
+variable B vector f_avborn*${bfac}
+variable B vector f_avborn*0.0315499354029305
+
+# Kinetic term
+
+variable kfac equal ${pconv}*${nktv2p}*atoms*${boltz}*${temp}/vol
+variable kfac equal 0.0001*${nktv2p}*atoms*${boltz}*${temp}/vol
+variable kfac equal 0.0001*1602176.5*atoms*${boltz}*${temp}/vol
+variable kfac equal 0.0001*1602176.5*atoms*8.617343e-05*${temp}/vol
+variable kfac equal 0.0001*1602176.5*atoms*8.617343e-05*1477.0/vol
+variable K11 equal 4.0*${kfac}
+variable K11 equal 4.0*1.00390440086865
+variable K22 equal 4.0*${kfac}
+variable K22 equal 4.0*1.00390440086865
+variable K33 equal 4.0*${kfac}
+variable K33 equal 4.0*1.00390440086865
+variable K44 equal 2.0*${kfac}
+variable K44 equal 2.0*1.00390440086865
+variable K55 equal 2.0*${kfac}
+variable K55 equal 2.0*1.00390440086865
+variable K66 equal 2.0*${kfac}
+variable K66 equal 2.0*1.00390440086865
+
+# Add F, K, and B together
+
+variable C11 equal v_F11+v_B[1]+v_K11
+variable C22 equal v_F22+v_B[2]+v_K22
+variable C33 equal v_F33+v_B[3]+v_K33
+variable C44 equal v_F44+v_B[4]+v_K44
+variable C55 equal v_F55+v_B[5]+v_K55
+variable C66 equal v_F66+v_B[6]+v_K66
+
+variable C12 equal v_F12+v_B[7]
+variable C13 equal v_F13+v_B[8]
+variable C14 equal v_F14+v_B[9]
+variable C15 equal v_F15+v_B[10]
+variable C16 equal v_F16+v_B[11]
+
+variable C23 equal v_F23+v_B[12]
+variable C24 equal v_F24+v_B[13]
+variable C25 equal v_F25+v_B[14]
+variable C26 equal v_F26+v_B[15]
+
+variable C34 equal v_F34+v_B[16]
+variable C35 equal v_F35+v_B[17]
+variable C36 equal v_F36+v_B[18]
+
+variable C45 equal v_F45+v_B[19]
+variable C46 equal v_F46+v_B[20]
+
+variable C56 equal v_F56+v_B[21]
+
+thermo		${nthermo}
+thermo		1500
+thermo_style custom step temp pe press density f_avt f_avp f_avpe v_F11 v_F22 v_F33 v_F44 v_F55 v_F66 v_F12 v_F13 v_F23 v_B[*8] v_B[12]
+
+thermo_modify norm no
+
+run ${nrun}
+run 150000
+Per MPI rank memory allocation (min/avg/max) = 3.808 | 3.808 | 3.809 Mbytes
+   Step          Temp          PotEng         Press         Density         f_avt          f_avp          f_avpe         v_F11          v_F22          v_F33          v_F44          v_F55          v_F66          v_F12          v_F13          v_F23          v_B[1]         v_B[2]         v_B[3]         v_B[4]         v_B[5]         v_B[6]         v_B[7]         v_B[8]        v_B[12]    
+         0   1496.4515     -1030.8279      1702.5821      2.2938491      0              0              0             -0             -0             -0             -0             -0             -0             -0             -0             -0              0              0              0              0              0              0              0              0              0            
+      1500   1488.0457     -1029.7336      235.49231      2.2938491      1491.6476     -209.95869     -4.1259067     -63.72574      -52.347237     -72.863469     -20.2529       -21.202225     -36.80768       15.820914      36.256996      27.837899      205.06161      205.28482      228.74061      53.516205      53.666764      76.479575      51.898427      28.841484      28.947835    
+      3000   1375.6945     -1032.3272     -1432.388       2.2938491      1483.7188     -14.944433     -4.1309886     -67.857182     -50.461537     -79.041956     -20.359329     -18.394118     -30.634049      16.973116      39.991949      29.200709      205.96072      205.57169      228.76797      53.760188      53.974806      76.829718      51.809223      28.715153      28.726595    
+      4500   1526.5784     -1034.4597      1558.1337      2.2938491      1482.7867     -70.886348     -4.1310256     -67.022382     -54.684704     -77.069485     -22.576461     -17.672784     -32.228898      21.458044      38.393569      27.72595       204.72251      205.88009      229.07903      53.899658      53.829006      76.717342      51.727843      28.636004      28.863718    
+      6000   1491.1951     -1030.0995      562.54917      2.2938491      1482.4806     -60.021349     -4.1307545     -66.909586     -58.886858     -80.148099     -22.601629     -19.09635      -33.473899      22.377747      38.855891      30.853996      204.70732      205.70649      229.01661      53.84119       53.800462      76.711553      51.690081      28.694904      28.797116    
+      7500   1330.8214     -1035.6828     -1407.4142      2.2938491      1480.7544     -63.898974     -4.1310393     -62.886575     -58.471219     -80.882593     -20.651266     -18.941729     -34.494541      18.287621      38.644547      32.466665      204.67832      205.92138      228.89129      53.887237      53.779706      76.803588      51.754653      28.661714      28.868533    
+      9000   1377.3139     -1030.6102     -814.50808      2.2938491      1480.0394     -57.969892     -4.1308955     -62.399927     -57.505746     -80.761377     -20.199819     -21.000829     -36.738929      17.319159      39.700869      31.315234      204.64296      206.17515      228.48224      53.911268      53.704831      76.8708        51.796155      28.641886      28.861077    
+     10500   1419.4538     -1032.4784     -554.39941      2.2938491      1481.1811     -7.9992199     -4.1309985     -59.045791     -61.164487     -82.861664     -19.890936     -21.168588     -35.873778      16.458244      37.100379      35.570692      204.9188       205.93531      228.57289      53.947197      53.739418      76.918077      51.784088      28.653206      28.87283     
+     12000   1442.3335     -1030.2902     -131.99922      2.2938491      1482.4991      25.724832     -4.1307257     -58.119089     -60.519191     -82.155615     -20.069823     -21.727839     -36.795312      16.944019      35.542297      35.788632      205.06536      205.89715      228.49105      53.949154      53.764738      76.945863      51.812548      28.698335      28.903557    
+     13500   1618.255      -1034.0691      448.39746      2.2938491      1482.9429      33.42958      -4.1306128     -59.840288     -61.599932     -82.215965     -20.598551     -21.492035     -36.443374      17.607876      36.241716      35.998172      205.07866      205.84943      228.61637      53.944979      53.774191      76.903895      51.792701      28.74114       28.89238     
+     15000   1364.3796     -1029.6878     -966.13025      2.2938491      1483.2726      65.784103     -4.1306007     -58.826126     -60.177687     -80.570212     -20.026628     -22.061421     -37.332987      16.618347      35.824117      34.991167      205.15731      205.79483      228.63407      53.929721      53.813353      76.896163      51.776923      28.752029      28.878669    
+     16500   1669.1757     -1031.0699      43.341777      2.2938491      1483.2491      18.99268      -4.1304591     -59.962016     -59.15211      -80.102432     -20.399129     -22.025441     -37.82746       17.082159      36.290705      33.775651      205.14266      205.7193       228.63038      53.925355      53.785453      76.855119      51.737872      28.759369      28.898142    
+     18000   1550.5382     -1027.3945     -1246.0289      2.2938491      1483.6491      5.7408759     -4.1303353     -59.35016      -58.728701     -78.818663     -20.150701     -21.942883     -37.891844      17.203814      35.337637      33.285126      205.13384      205.6063       228.57531      53.891378      53.769275      76.832714      51.74568       28.791121      28.877624    
+     19500   1629.5036     -1036.9849     -451.26178      2.2938491      1484.1226      27.288331     -4.1304459     -58.665989     -60.109261     -78.714857     -20.404554     -21.983442     -37.992827      17.117122      34.608111      34.643094      205.23998      205.53366      228.59186      53.890849      53.787956      76.856299      51.736162      28.786354      28.85888     
+     21000   1472.5544     -1032.859      -20.186692      2.2938491      1483.3486      19.365496     -4.130639      -59.030496     -61.687931     -79.499878     -21.045487     -21.978669     -37.750071      17.282482      34.752705      35.830146      205.166        205.4977       228.68839      53.897034      53.798516      76.833481      51.716388      28.777538      28.853221    
+     22500   1538.3331     -1029.4222     -1516.1779      2.2938491      1483.9369      9.3663668     -4.1304658     -59.601342     -61.528294     -79.886775     -21.058116     -21.744815     -37.415441      17.458006      35.03524       35.490302      205.15957      205.3737       228.66857      53.875938      53.82329       76.813455      51.710539      28.807394      28.846491    
+     24000   1640.6306     -1032.8747      1820.5076      2.2938491      1484.3582     -2.9605818     -4.1303985     -60.752912     -62.308755     -80.507722     -21.295171     -21.728498     -37.85529       17.636088      35.38702       36.141494      205.19032      205.28915      228.69633      53.859405      53.858117      76.802512      51.728172      28.822365      28.83436     
+     25500   1432.5405     -1036.4177      165.16737      2.2938491      1483.2229      8.3729002     -4.1307362     -60.653401     -61.891943     -80.020623     -21.215377     -21.694568     -37.770769      17.468376      35.128883      36.013452      205.2687       205.29914      228.65445      53.868129      53.866433      76.831986      51.734064      28.809762      28.823143    
+     27000   1459.7165     -1032.2704      555.49626      2.2938491      1483.5999      29.734336     -4.1307773     -60.348436     -62.451484     -79.397912     -21.536942     -21.312644     -37.473352      18.07619       34.322981      36.063688      205.28479      205.36871      228.6014       53.882785      53.860318      76.843783      51.736186      28.791218      28.824958    
+     28500   1398.7866     -1032.325      -228.86327      2.2938491      1482.9241      10.135953     -4.1308163     -60.923204     -62.1935       -80.289996     -21.326799     -21.465421     -37.781979      17.525986      35.112803      36.122375      205.33196      205.38849      228.51467      53.877397      53.85885       76.855869      51.748421      28.791318      28.810646    
+     30000   1609.4626     -1026.1198      2151.4352      2.2938491      1482.737      -6.9747499     -4.130764      -62.14162      -62.578377     -79.864982     -21.683154     -21.501264     -37.647952      18.064145      35.592848      35.670682      205.30816      205.42759      228.45924      53.874997      53.845931      76.855299      51.757648      28.798886      28.822951    
+     31500   1535.1988     -1030.7627      1962.4562      2.2938491      1482.9354     -2.7241836     -4.1306143     -61.870375     -62.851578     -80.524128     -21.560593     -21.908782     -38.604429      18.110966      35.564598      36.054336      205.32395      205.40536      228.48839      53.874999      53.854825      76.856925      51.764937      28.810228      28.831593    
+     33000   1570.1208     -1026.2494      351.76291      2.2938491      1482.996      -7.4807931     -4.130577      -62.238722     -63.288756     -80.80606      -21.615247     -21.67204      -38.37626       18.053097      35.862534      36.372658      205.33168      205.41606      228.43691      53.871561      53.849411      76.854679      51.770903      28.813329      28.832923    
+     34500   1432.3272     -1031.7548      419.21972      2.2938491      1482.7892     -28.425324     -4.1304667     -61.926882     -63.333125     -80.201249     -21.557493     -21.477997     -38.188053      17.990156      35.484765      36.40502       205.32852      205.36594      228.42193      53.858032      53.85339       76.845155      51.776258      28.810311      28.83193     
+     36000   1461.1221     -1031.0936     -732.09091      2.2938491      1482.7576     -17.70291      -4.1306165     -62.179266     -62.986391     -81.351014     -21.399698     -21.423609     -38.39933       17.389924      36.483096      36.528136      205.36025      205.37113      228.45226      53.869219      53.85851       76.853637      51.780873      28.812037      28.835983    
+     37500   1504.8525     -1035.0799      1917.6077      2.2938491      1482.2878     -23.877209     -4.1306315     -62.332808     -63.43488      -81.773513     -21.40584      -21.375369     -38.287661      17.372388      36.472678      37.074729      205.36817      205.37669      228.40654      53.854172      53.855291      76.849674      51.775051      28.80071       28.818624    
+     39000   1467.8385     -1033.4844      685.3059       2.2938491      1481.8721     -31.824125     -4.1307881     -63.029639     -63.482571     -82.632663     -21.710699     -21.140028     -38.056647      17.507416      37.185033      37.136598      205.33141      205.38158      228.41356      53.864319      53.853944      76.842991      51.764685      28.788943      28.816327    
+     40500   1471.3714     -1035.0313     -661.11589      2.2938491      1482.1911     -28.660441     -4.1307331     -63.073554     -63.301254     -81.939449     -21.849646     -21.333366     -38.459438      17.701055      36.929221      36.777905      205.3174       205.38828      228.42064      53.864766      53.857226      76.830391      51.764266      28.789323      28.813992    
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+     45000   1490.388      -1032.0658      956.44619      2.2938491      1482.0953     -16.260449     -4.1307284     -62.718709     -61.819139     -80.292247     -21.55464      -21.249523     -38.355562      17.650135      36.482629      35.521216      205.36793      205.41743      228.39993      53.868999      53.866369      76.841723      51.766771      28.793869      28.808214    
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+     54000   1533.7764     -1028.7613      1714.1927      2.2938491      1481.7208     -28.620488     -4.1308301     -63.113526     -61.903055     -79.382866     -21.730147     -21.21458      -38.316562      18.001225      36.474036      34.681959      205.34377      205.31381      228.39872      53.84474       53.889496      76.812664      51.743856      28.802121      28.781409    
+     55500   1523.4727     -1033.3641     -612.71038      2.2938491      1481.8812     -36.263593     -4.1307128     -63.926005     -61.676301     -79.572696     -21.935651     -21.124984     -38.120805      18.30654       36.789152      34.374772      205.31795      205.35529      228.36668      53.847443      53.882195      76.806901      51.74734       28.814592      28.796537    
+     57000   1491.3678     -1026.9983     -1119.4609      2.2938491      1481.9455     -36.326068     -4.1306892     -63.595683     -61.564985     -79.974258     -21.822985     -21.136666     -38.16275       18.083171      36.766293      34.707154      205.29618      205.33458      228.38626      53.852279      53.878924      76.797511      51.735536      28.815462      28.802463    
+     58500   1438.7756     -1027.9678     -1657.13        2.2938491      1481.9051     -46.49998      -4.1306702     -63.970101     -61.372119     -79.511332     -21.995264     -21.032781     -38.038112      18.401226      36.639522      34.227378      205.29966      205.32376      228.38361      53.852024      53.875838      76.788068      51.734772      28.81576       28.803892    
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+     61500   1505.9305     -1036.2556      132.06247      2.2938491      1481.6293     -37.731588     -4.1308223     -64.381464     -61.674639     -80.188334     -22.158723     -21.108889     -38.248855      18.390358      37.059536      34.455424      205.23517      205.35912      228.41484      53.864166      53.876015      76.794352      51.722323      28.804043      28.801179    
+     63000   1534.39       -1039.4484      1046.653       2.2938491      1481.7949     -33.380601     -4.1308464     -64.068931     -61.368649     -79.704263     -22.130922     -21.067286     -38.215994      18.495768      36.761782      34.189797      205.22412      205.35391      228.43945      53.869115      53.87449       76.793337      51.712686      28.794684      28.800456    
+     64500   1361.7518     -1030.5694      790.72852      2.2938491      1481.8251     -28.691877     -4.1308571     -64.06363      -61.273278     -79.676705     -22.16565      -21.02496      -38.172259      18.638855      36.719131      34.006715      205.20559      205.35747      228.42261      53.874341      53.871631      76.797534      51.715519      28.789202      28.800286    
+     66000   1493.9592     -1034.8315     -83.381519      2.2938491      1481.8804     -28.444673     -4.130839      -63.871998     -60.922315     -79.543208     -22.084939     -21.051796     -38.178075      18.469097      36.653501      33.983218      205.17353      205.37012      228.4333       53.873209      53.87128       76.793735      51.715772      28.787185      28.799271    
+     67500   1421.276      -1033.8109     -435.15037      2.2938491      1482.0268     -15.717566     -4.1308595     -63.961701     -61.265171     -79.32614      -22.181352     -20.923325     -37.927752      18.58702       36.575619      34.041641      205.20462      205.4057       228.41483      53.873248      53.867409      76.806453      51.725025      28.781635      28.790933    
+     69000   1462.71       -1031.786       2044.924       2.2938491      1482.0808     -12.41913      -4.1308487     -63.537939     -61.572781     -79.813735     -22.037844     -20.940539     -37.978104      18.246032      36.52598       34.631512      205.21991      205.43641      228.3772       53.872474      53.864337      76.817521      51.736948      28.777643      28.790877    
+     70500   1460.7684     -1032.5687     -950.70337      2.2938491      1482.2232     -6.1090924     -4.1308194     -62.959394     -61.457796     -79.687401     -21.885475     -20.919469     -37.921646      18.034683      36.313758      34.737829      205.22464      205.41986      228.36249      53.872577      53.869324      76.818318      51.735068      28.780852      28.790481    
+     72000   1421.4484     -1031.353       1648.2423      2.2938491      1482.362      -8.171728      -4.1308339     -62.919483     -61.526828     -79.571975     -21.913281     -20.822948     -37.684888      18.014821      36.170823      34.809531      205.23354      205.40265      228.37137      53.876829      53.868192      76.821146      51.735902      28.781575      28.799457    
+     73500   1752.498      -1034.2169      1469.9503      2.2938491      1482.5906     -3.8737403     -4.130845      -62.630533     -61.309844     -79.729568     -21.758626     -20.825548     -37.860657      17.748076      36.259904      34.845837      205.22997      205.41547      228.3844       53.883713      53.868296      76.824464      51.735899      28.783023      28.803298    
+     75000   1520.6212     -1036.5004      837.2324       2.2938491      1482.4238     -0.1913038     -4.1308831     -62.821147     -61.828489     -79.567323     -21.889326     -20.789721     -37.714104      17.879632      36.22222       34.919953      205.2442       205.41386      228.37542      53.88291       53.867274      76.830786      51.73158       28.778935      28.794923    
+     76500   1439.6706     -1034.3536      3.867216       2.2938491      1482.3799      2.9201733     -4.1309078     -63.110409     -61.628579     -79.646303     -21.943803     -20.784043     -37.709136      18.090962      36.339502      34.640705      205.22882      205.4377       228.37991      53.889722      53.867867      76.832127      51.730291      28.776106      28.800613    
+     78000   1472.2878     -1032.0488      606.92009      2.2938491      1482.4315      4.0162921     -4.1308864     -63.18742      -61.476216     -79.518345     -21.915006     -20.795344     -37.685095      18.160875      36.317768      34.562962      205.21304      205.4681       228.35132      53.888419      53.860959      76.832795      51.726368      28.769804      28.803835    
+     79500   1512.5998     -1031.4782     -608.33112      2.2938491      1482.4683     -4.9946179     -4.1308672     -63.136709     -61.38976      -79.342774     -21.877029     -20.790716     -37.765995      18.082202      36.307384      34.529887      205.20173      205.45621      228.33612      53.884127      53.85096       76.827797      51.725854      28.764443      28.800151    
+     81000   1517.4109     -1028.3826     -2043.4874      2.2938491      1482.2404     -19.291403     -4.130792      -62.826972     -61.57491      -78.919307     -21.815485     -20.773717     -37.72361       18.034102      35.870919      34.590596      205.18765      205.42705      228.3524       53.878666      53.848387      76.814541      51.723458      28.771787      28.801959    
+     82500   1495.0416     -1034.9971     -919.28281      2.2938491      1482.5918     -7.0685741     -4.1308239     -62.741622     -61.394991     -78.779816     -21.795693     -20.713253     -37.628978      18.028438      35.854382      34.286915      205.18358      205.42059      228.39152      53.88507       53.855289      76.812978      51.718793      28.771939      28.803997    
+     84000   1491.0232     -1032.0478      1693.2093      2.2938491      1482.6179     -13.503477     -4.1306843     -62.623399     -61.545116     -78.875891     -21.831602     -20.760705     -37.783204      18.049826      35.698982      34.461373      205.18823      205.41432      228.37952      53.880292      53.848427      76.812319      51.723745      28.776002      28.809842    
+     85500   1432.7633     -1032.698      -881.37505      2.2938491      1482.5743     -10.555756     -4.1306695     -62.232152     -61.412377     -78.830213     -21.727847     -20.801103     -37.812275      17.923531      35.499394      34.546639      205.19889      205.41789      228.36824      53.880011      53.849407      76.819282      51.727384      28.780783      28.812392    
+     87000   1485.3288     -1032.6691      158.89155      2.2938491      1482.5535     -6.3950299     -4.1307187     -62.169286     -61.063223     -78.970108     -21.61197      -20.763121     -37.82023       17.757088      35.636063      34.438868      205.1894       205.43526      228.38369      53.883498      53.850233      76.819949      51.726626      28.776566      28.814967    
+     88500   1504.1685     -1034.896      -576.81489      2.2938491      1482.5577     -4.2302198     -4.1307273     -62.060242     -60.91541      -79.120582     -21.5292       -20.789763     -37.890171      17.627385      35.769308      34.444455      205.17713      205.41733      228.41274      53.884038      53.851418      76.815226      51.720575      28.778578      28.81437     
+     90000   1449.8972     -1033.1249      16.828339      2.2938491      1482.5956     -3.7681039     -4.1306958     -62.088756     -60.725318     -79.170616     -21.492856     -20.734831     -37.741223      17.584396      35.868249      34.318289      205.18548      205.4084       228.40148      53.880047      53.853611      76.816207      51.723692      28.779781      28.809322    
+     91500   1416.2681     -1033.1616     -16.270943      2.2938491      1482.4743     -10.282897     -4.1306355     -62.133545     -60.706158     -79.069992     -21.526357     -20.751961     -37.744268      17.678691      35.77502       34.270056      205.20409      205.40965      228.38688      53.875395      53.853283      76.818389      51.731399      28.784679      28.812085    
+     93000   1641.0262     -1032.9652      1541.4778      2.2938491      1482.7239     -0.21530915    -4.1306987     -62.103472     -60.524542     -78.94244      -21.416169     -20.762777     -37.724968      17.503079      35.79639       34.254575      205.21819      205.4208       228.38518      53.874775      53.859201      76.82538       51.73286       28.787014      28.806284    
+     94500   1446.894      -1033.0546     -1172.8149      2.2938491      1482.6464      3.4467336     -4.1307822     -62.347354     -60.242764     -79.472893     -21.34953      -20.717759     -37.687715      17.289476      36.186844      34.277361      205.23165      205.43019      228.39821      53.884069      53.865596      76.827934      51.732077      28.786882      28.805655    
+     96000   1542.079      -1029.6926      322.45446      2.2938491      1482.5441      4.6485293     -4.1308136     -62.206988     -59.973518     -79.080994     -21.288972     -20.760823     -37.729071      17.259751      36.128248      33.998066      205.24388      205.42381      228.41608      53.886007      53.867776      76.82741       51.731615      28.791259      28.805397    
+     97500   1487.9454     -1034.7172      820.51649      2.2938491      1482.5632      8.5386652     -4.1308234     -62.143296     -60.101635     -78.931963     -21.290736     -20.716267     -37.692871      17.462016      36.002029      33.918161      205.26305      205.43429      228.40827      53.888433      53.870451      76.826913      51.728767      28.791481      28.804241    
+     99000   1368.2594     -1031.2037      593.35668      2.2938491      1482.6064      5.0925632     -4.1307682     -61.963501     -60.016279     -78.857674     -21.245113     -20.75973      -37.759628      17.293147      36.020666      33.897023      205.26324      205.41903      228.40538      53.882522      53.868615      76.826529      51.734223      28.797165      28.804278    
+    100500   1442.5153     -1033.8773     -538.06378      2.2938491      1482.5806      8.0051295     -4.1307853     -61.807415     -59.816464     -78.885211     -21.182274     -20.821701     -37.887086      17.136467      36.03321       33.886956      205.29244      205.41979      228.40702      53.882321      53.875874      76.834725      51.739661      28.801012      28.804575    
+    102000   1523.8256     -1030.5549      1412.4566      2.2938491      1482.5866      4.0411856     -4.1307569     -61.444398     -59.781654     -78.484191     -21.18101      -20.822776     -37.865635      17.152952      35.720218      33.798513      205.2959       205.39482      228.41979      53.878609      53.877207      76.830098      51.741804      28.807055      28.805499    
+    103500   1577.9333     -1030.2793      16.968578      2.2938491      1482.4554      1.2961629     -4.1307672     -61.397825     -59.829587     -78.4479       -21.161504     -20.867524     -37.888147      17.149447      35.662363      33.851317      205.28757      205.3981       228.43413      53.882435      53.873014      76.827589      51.735462      28.805202      28.810239    
+    105000   1337.0075     -1031.8541     -2721.9544      2.2938491      1482.4268     -4.353932      -4.1307412     -61.705223     -59.747259     -78.609622     -21.165441     -20.851207     -37.876114      17.14923       35.951734      33.665587      205.27089      205.39074      228.43789      53.879034      53.870275      76.822978      51.73248       28.802281      28.81082     
+    106500   1422.8946     -1030.8343     -800.38058      2.2938491      1482.5115     -4.0049886     -4.1307542     -61.643384     -59.644844     -78.475169     -21.104781     -20.828498     -37.805234      16.983794      35.924403      33.682427      205.27511      205.39208      228.44888      53.881421      53.873402      76.821913      51.730452      28.801513      28.816076    
+    108000   1576.0145     -1032.7976      973.46949      2.2938491      1482.6158      3.0627527     -4.1307693     -61.632096     -59.704639     -78.39173      -21.106554     -20.866293     -37.84322       16.999887      35.7367        33.736853      205.27847      205.39567      228.46373      53.883841      53.8794        76.823598      51.724192      28.797812      28.814282    
+    109500   1469.798      -1035.4088     -1513.3569      2.2938491      1482.5815     -2.3554776     -4.1307587     -61.409226     -59.368417     -78.056976     -20.987396     -20.922787     -37.905832      16.80989       35.603164      33.571735      205.29739      205.39186      228.45528      53.881647      53.883201      76.826509      51.727265      28.803221      28.816387    
+    111000   1450.1364     -1034.8692      535.01425      2.2938491      1482.5086     -4.9493018     -4.1307925     -61.853187     -59.298301     -78.058449     -21.0476       -20.870886     -37.809302      16.931849      35.815648      33.395258      205.30581      205.38706      228.47139      53.885853      53.883453      76.822939      51.72578       28.798242      28.817665    
+    112500   1449.2612     -1032.1626     -707.9713       2.2938491      1482.6231     -5.6051571     -4.1307318     -61.617376     -59.400658     -77.86748      -21.058008     -20.900491     -37.885275      16.941367      35.595081      33.457412      205.31006      205.37483      228.46421      53.884923      53.884787      76.818386      51.725453      28.799728      28.818511    
+    114000   1472.8275     -1037.0664     -442.38894      2.2938491      1482.8034     -1.1760851     -4.13075       -61.604652     -59.42193      -77.729625     -21.108945     -20.839988     -37.816934      17.027186      35.528809      33.333712      205.2996       205.40083      228.47441      53.889449      53.885434      76.822691      51.72532       28.799205      28.817456    
+    115500   1412.2073     -1033.3813     -859.54093      2.2938491      1482.7115     -6.3971107     -4.1307164     -61.582698     -59.540524     -77.958489     -21.065292     -20.841779     -37.81416       17.014851      35.663213      33.266402      205.30868      205.39757      228.44955      53.887583      53.882631      76.821441      51.730925      28.798319      28.820824    
+    117000   1460.2307     -1028.9074     -1164.6613      2.2938491      1482.657      -7.8697826     -4.1307244     -61.82235      -59.692597     -77.850871     -21.124418     -20.764516     -37.690786      17.155656      35.649724      33.269516      205.30451      205.41455      228.45187      53.893125      53.885988      76.81911       51.730761      28.798798      28.824658    
+    118500   1493.0731     -1028.7066     -260.29362      2.2938491      1482.7469     -1.8511441     -4.1307413     -61.826554     -59.86035      -77.828964     -21.126638     -20.753378     -37.660607      17.198524      35.664955      33.285591      205.31841      205.42978      228.43324      53.895373      53.888281      76.82351       51.731769      28.799645      28.824431    
+    120000   1345.6123     -1029.9346     -1895.5256      2.2938491      1482.7843     -4.5972195     -4.1307269     -61.669058     -59.838425     -77.745234     -21.161305     -20.848334     -37.830906      17.174454      35.604439      33.297851      205.32668      205.43762      228.42017      53.889381      53.883438      76.823854      51.733939      28.794303      28.822327    
+    121500   1407.0748     -1031.8136      426.75808      2.2938491      1482.8284     -1.6468876     -4.1307603     -61.64701      -59.903233     -77.693914     -21.163628     -20.835781     -37.828167      17.171387      35.563809      33.348664      205.34563      205.44066      228.4023       53.88813       53.886137      76.827345      51.735371      28.794168      28.819736    
+    123000   1526.2861     -1032.537       852.79109      2.2938491      1482.9332      5.0560365     -4.1307796     -61.724187     -59.904131     -77.473899     -21.179869     -20.815648     -37.857571      17.267887      35.516275      33.238968      205.36759      205.43856      228.38631      53.885394      53.886842      76.832314      51.732243      28.791888      28.813868    
+    124500   1529.8037     -1031.1582     -92.453284      2.2938491      1483.0597      8.0257434     -4.130767      -61.73912      -59.872674     -77.532647     -21.149928     -20.801849     -37.741413      17.188         35.59366       33.235229      205.37362      205.43069      228.39692      53.88626       53.886586      76.834567      51.73587       28.793201      28.81626     
+    126000   1496.3891     -1033.1452     -367.03965      2.2938491      1483.0771      4.6045133     -4.1307269     -61.729431     -59.954414     -77.338248     -21.179207     -20.784619     -37.762061      17.353033      35.439541      33.189469      205.36796      205.44072      228.37772      53.885265      53.881811      76.830859      51.738138      28.792247      28.818739    
+    127500   1466.1306     -1030.612      -926.29759      2.2938491      1483.133       11.366773     -4.1307722     -61.602447     -59.920526     -77.282372     -21.159672     -20.75159      -37.719968      17.307656      35.296921      33.236486      205.37779      205.44691      228.38745      53.887086      53.885763      76.836326      51.737488      28.792599      28.815257    
+    129000   1569.3651     -1032.9186     -442.35004      2.2938491      1483.1369      10.328658     -4.1307387     -61.543466     -59.942662     -77.483904     -21.119911     -20.722378     -37.671723      17.281249      35.232627      33.459675      205.36599      205.43931      228.40108      53.884216      53.882413      76.831442      51.737409      28.790919      28.811477    
+    130500   1421.911      -1031.8139     -758.70123      2.2938491      1483.0449      11.4085       -4.1307613     -61.333773     -59.934246     -77.426746     -21.113826     -20.713965     -37.674443      17.157344      35.141168      33.569733      205.36146      205.44547      228.4022       53.886232      53.879268      76.832738      51.73627       28.786769      28.811493    
+    132000   1524.2191     -1037.407      -480.85722      2.2938491      1482.8528      8.9287162     -4.1308006     -61.561432     -60.092757     -77.742507     -21.167795     -20.674863     -37.639706      17.29371       35.275171      33.678108      205.36428      205.45116      228.4058       53.889052      53.879475      76.834536      51.73562       28.786514      28.811264    
+    133500   1494.6866     -1034.7465      416.3259       2.2938491      1482.8997      8.7918538     -4.1307995     -61.539391     -60.210309     -78.095947     -21.12506      -20.675829     -37.641619      17.068859      35.348266      34.049804      205.37443      205.45053      228.39031      53.888328      53.87864       76.837876      51.741192      28.786138      28.811558    
+    135000   1569.7047     -1036.5833      1648.5811      2.2938491      1482.8373      16.413757     -4.1308862     -61.379715     -60.19875      -77.885213     -21.077149     -20.659689     -37.571815      17.039133      35.160383      34.027006      205.38045      205.47385      228.40044      53.89379       53.883916      76.84446       51.74077       28.782168      28.811503    
+    136500   1434.076      -1032.3999      1440.6873      2.2938491      1482.8065      20.877471     -4.130942      -61.250129     -60.36518      -77.797762     -21.173422     -20.644652     -37.555746      17.168354      34.98673       34.050232      205.39567      205.46987      228.41208      53.893145      53.888561      76.850201      51.742217      28.782951      28.809364    
+    138000   1435.6229     -1027.2932     -1994.0334      2.2938491      1482.9676      28.338068     -4.1309771     -61.286555     -60.502324     -77.929763     -21.144817     -20.627874     -37.5188        16.99209       35.098588      34.233379      205.38967      205.48076      228.41949      53.897481      53.889052      76.852273      51.743864      28.782553      28.811336    
+    139500   1351.2102     -1032.4433     -239.90235      2.2938491      1482.9605      27.292315     -4.1309341     -61.209087     -60.465858     -77.765563     -21.106356     -20.671478     -37.691344      16.943971      35.047976      34.174565      205.38424      205.48042      228.42161      53.896767      53.885832      76.847548      51.746591      28.779555      28.812114    
+    141000   1467.5087     -1031.9354     -532.99883      2.2938491      1482.8932      24.307649     -4.1309051     -61.070518     -60.441795     -77.624715     -21.086802     -20.640868     -37.683803      17.017529      34.883575      34.096205      205.37075      205.48554      228.42021      53.896931      53.882672      76.844472      51.745488      28.777347      28.815227    
+    142500   1426.8036     -1029.0269      475.29365      2.2938491      1482.9486      28.873848     -4.1309222     -61.253743     -60.394307     -77.623948     -21.117683     -20.666512     -37.724806      17.009433      34.985626      34.037536      205.38057      205.50055      228.40554      53.898614      53.880885      76.846518      51.744358      28.772507      28.8159      
+    144000   1442.207      -1031.8281      666.41114      2.2938491      1482.9324      27.849865     -4.1309475     -61.168217     -60.212673     -77.584118     -21.079119     -20.692903     -37.826824      16.878262      35.048543      34.002324      205.37899      205.51754      228.39212      53.90079       53.88167       76.847699      51.746645      28.771418      28.817434    
+    145500   1513.7861     -1032.8894      103.68291      2.2938491      1483.1433      26.889484     -4.1309369     -61.076852     -60.104649     -77.709917     -21.033322     -20.670939     -37.779427      16.717574      35.122343      34.057639      205.3625       205.52972      228.37916      53.90269       53.879604      76.847902      51.74393       28.76916       28.820449    
+    147000   1403.8295     -1038.4747      125.48856      2.2938491      1483.0944      25.436764     -4.1309291     -61.058221     -60.015165     -77.827606     -21.025708     -20.75728      -37.905513      16.756237      35.091941      34.043829      205.36839      205.52553      228.38543      53.902592      53.879578      76.848283      51.744624      28.771608      28.822339    
+    148500   1570.4334     -1030.4725      1176.9001      2.2938491      1482.9036      26.018243     -4.1309919     -60.988967     -59.970975     -77.596029     -21.062881     -20.789165     -38.050798      16.784906      34.917316      34.005084      205.36511      205.5204       228.39472      53.905268      53.883557      76.849572      51.742284      28.771597      28.820426    
+    150000   1637.0679     -1032.2165      1094.5581      2.2938491      1482.9569      27.608241     -4.1310012     -61.014673     -59.868323     -77.559954     -21.028486     -20.762668     -37.995752      16.75055       34.948738      33.9703        205.36993      205.53181      228.3843       53.905331      53.882296      76.852069      51.742975      28.773161      28.820754    
+Loop time of 23.1063 on 4 procs for 150000 steps with 250 atoms
+
+Performance: 429.638 ns/day, 0.056 hours/ns, 6491.724 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 13.514     | 15.049     | 16.345     |  27.6 | 65.13
+Neigh   | 0.22265    | 0.23987    | 0.26064    |   2.8 |  1.04
+Comm    | 2.4163     | 3.7264     | 5.2764     |  56.0 | 16.13
+Output  | 0.0032872  | 0.0035512  | 0.0043178  |   0.7 |  0.02
+Modify  | 3.7671     | 3.7877     | 3.8007     |   0.7 | 16.39
+Other   |            | 0.2998     |            |       |  1.30
+
+Nlocal:           62.5 ave          88 max          40 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+Nghost:         432.75 ave         543 max         326 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:       1650.5 ave        2334 max        1048 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+
+Total # of neighbors = 6602
+Ave neighs/atom = 26.408
+Neighbor list builds = 2667
+Dangerous builds = 0
+
+# Output final values
+
+include final_output.in
+# Average moduli for cubic crystals
+
+variable C11cubic equal (${C11}+${C22}+${C33})/3.0
+variable C11cubic equal (148.370873646034+${C22}+${C33})/3.0
+variable C11cubic equal (148.370873646034+149.679104177467+${C33})/3.0
+variable C11cubic equal (148.370873646034+149.679104177467+154.839963498785)/3.0
+variable C12cubic equal (${C12}+${C13}+${C23})/3.0
+variable C12cubic equal (68.4935246016777+${C13}+${C23})/3.0
+variable C12cubic equal (68.4935246016777+63.7218992685599+${C23})/3.0
+variable C12cubic equal (68.4935246016777+63.7218992685599+62.7910539636263)/3.0
+variable C44cubic equal (${C44}+${C55}+${C66})/3.0
+variable C44cubic equal (34.8846541689484+${C55}+${C66})/3.0
+variable C44cubic equal (34.8846541689484+35.1274361331555+${C66})/3.0
+variable C44cubic equal (34.8846541689484+35.1274361331555+40.8641262264389)/3.0
+
+variable bulkmodulus equal (${C11cubic}+2*${C12cubic})/3.0
+variable bulkmodulus equal (150.963313774095+2*${C12cubic})/3.0
+variable bulkmodulus equal (150.963313774095+2*65.0021592779546)/3.0
+variable shearmodulus1 equal ${C44cubic}
+variable shearmodulus1 equal 36.9587388428476
+variable shearmodulus2 equal (${C11cubic}-${C12cubic})/2.0
+variable shearmodulus2 equal (150.963313774095-${C12cubic})/2.0
+variable shearmodulus2 equal (150.963313774095-65.0021592779546)/2.0
+variable poissonratio equal 1.0/(1.0+${C11cubic}/${C12cubic})
+variable poissonratio equal 1.0/(1.0+150.963313774095/${C12cubic})
+variable poissonratio equal 1.0/(1.0+150.963313774095/65.0021592779546)
+
+# For Stillinger-Weber silicon, the analytical results
+# are known to be (E. R. Cowley, 1988):
+#               C11 = 151.4 GPa
+#               C12 = 76.4 GPa
+#               C44 = 56.4 GPa
+
+#print "========================================="
+#print "Components of the Elastic Constant Tensor"
+#print "========================================="
+
+print "Elastic Constant C11 = ${C11} ${cunits}"
+Elastic Constant C11 = 148.370873646034 GPa
+print "Elastic Constant C22 = ${C22} ${cunits}"
+Elastic Constant C22 = 149.679104177467 GPa
+print "Elastic Constant C33 = ${C33} ${cunits}"
+Elastic Constant C33 = 154.839963498785 GPa
+
+print "Elastic Constant C12 = ${C12} ${cunits}"
+Elastic Constant C12 = 68.4935246016777 GPa
+print "Elastic Constant C13 = ${C13} ${cunits}"
+Elastic Constant C13 = 63.7218992685599 GPa
+print "Elastic Constant C23 = ${C23} ${cunits}"
+Elastic Constant C23 = 62.7910539636263 GPa
+
+print "Elastic Constant C44 = ${C44} ${cunits}"
+Elastic Constant C44 = 34.8846541689484 GPa
+print "Elastic Constant C55 = ${C55} ${cunits}"
+Elastic Constant C55 = 35.1274361331555 GPa
+print "Elastic Constant C66 = ${C66} ${cunits}"
+Elastic Constant C66 = 40.8641262264389 GPa
+
+print "Elastic Constant C14 = ${C14} ${cunits}"
+Elastic Constant C14 = 6.92404731313863 GPa
+print "Elastic Constant C15 = ${C15} ${cunits}"
+Elastic Constant C15 = -0.241854528091832 GPa
+print "Elastic Constant C16 = ${C16} ${cunits}"
+Elastic Constant C16 = -0.348583506816062 GPa
+
+print "Elastic Constant C24 = ${C24} ${cunits}"
+Elastic Constant C24 = -8.12880441353851 GPa
+print "Elastic Constant C25 = ${C25} ${cunits}"
+Elastic Constant C25 = 0.489292435379784 GPa
+print "Elastic Constant C26 = ${C26} ${cunits}"
+Elastic Constant C26 = 0.823159952503936 GPa
+
+print "Elastic Constant C34 = ${C34} ${cunits}"
+Elastic Constant C34 = 0.696244884461012 GPa
+print "Elastic Constant C35 = ${C35} ${cunits}"
+Elastic Constant C35 = 0.0721961245198595 GPa
+print "Elastic Constant C36 = ${C36} ${cunits}"
+Elastic Constant C36 = -0.201416093587799 GPa
+
+print "Elastic Constant C45 = ${C45} ${cunits}"
+Elastic Constant C45 = -0.310665193707046 GPa
+print "Elastic Constant C46 = ${C46} ${cunits}"
+Elastic Constant C46 = -0.491041219509184 GPa
+print "Elastic Constant C56 = ${C56} ${cunits}"
+Elastic Constant C56 = 7.93280717781775 GPa
+
+print "========================================="
+=========================================
+print "Average properties for a cubic crystal"
+Average properties for a cubic crystal
+print "========================================="
+=========================================
+
+print "Bulk Modulus = ${bulkmodulus} ${cunits}"
+Bulk Modulus = 93.6558774433347 GPa
+print "Shear Modulus 1 = ${shearmodulus1} ${cunits}"
+Shear Modulus 1 = 36.9587388428476 GPa
+print "Shear Modulus 2 = ${shearmodulus2} ${cunits}"
+Shear Modulus 2 = 42.9805772480702 GPa
+print "Poisson Ratio = ${poissonratio}"
+Poisson Ratio = 0.300984033972359
+
+# summarize sampling protocol
+
+variable tmp equal atoms
+print "Number of atoms = ${tmp}"
+Number of atoms = 250
+print "Stress sampling interval = ${nevery}"
+Stress sampling interval = 10
+variable tmp equal ${nrun}/${nevery}
+variable tmp equal 150000/${nevery}
+variable tmp equal 150000/10
+print "Stress sample count = ${tmp}"
+Stress sample count = 15000
+print "Born sampling interval = ${neveryborn}"
+Born sampling interval = 100
+variable tmp equal ${nrun}/${neveryborn}
+variable tmp equal 150000/${neveryborn}
+variable tmp equal 150000/100
+print "Born sample count = ${tmp}"
+Born sample count = 1500
+Total wall time: 0:00:25