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Merge branch 'develop' of github.com:lammps/lammps into kk_update_4.0

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This commit is contained in:
Stan Gerald Moore
2023-07-14 17:59:15 -06:00
parent 3c09aa26f9 2090d33d5f
commit 78470febbd
524 changed files with 3196 additions and 4029 deletions
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615
cmake/CMakeLists.jpeg
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@ -1,615 +0,0 @@
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()

741
cmake/CMakeLists.png
View File

@ -1,741 +0,0 @@
# 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

195
cmake/CMakeLists.zlib
View File

@ -1,195 +0,0 @@
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()

2
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -89,7 +89,7 @@ else()
if(CMAKE_REQUEST_PIC)
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR} EXCLUDE_FROM_ALL)
set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src

2
doc/src/Bibliography.rst
View File

@ -203,7 +203,7 @@ Bibliography
A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)
**(CasP)**
CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html
CasP webpage: http://www.casp-program.org/
**(Cawkwell2012)**
A.\ M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012).

4
doc/src/Howto_2d.rst
View File

@ -13,9 +13,9 @@ box with a single z plane of atoms - e.g.
.. code-block:: LAMMPS
create box 1 -10 10 -10 10 -0.25 0.25
create_box 1 -10 10 -10 10 -0.25 0.25
If using the :doc:`read data <read_data>` command to read in a file of
If using the :doc:`read_data <read_data>` command to read in a file of
atom coordinates, set the "zlo zhi" values to be finite but narrow,
similar to the create_box command settings just described. For each
atom in the file, assign a z coordinate so it falls inside the

18
doc/src/Howto_bpm.rst
View File

@ -79,9 +79,9 @@ As bonds can be broken between neighbor list builds, the
bond styles. There are two possible settings which determine how pair
interactions work between bonded particles. First, one can overlay
pair forces with bond forces such that all bonded particles also
feel pair interactions. This can be accomplished by using the *overlay/pair*
keyword present in all bpm bond styles and by using the following special
bond settings
feel pair interactions. This can be accomplished by setting the *overlay/pair*
keyword present in all bpm bond styles to *yes* and requires using the
following special bond settings
.. code-block:: LAMMPS
@ -107,7 +107,17 @@ bond lists is expensive. By setting the lj weight for 1-2 bonds to
zero, this turns off pairwise interactions. Even though there are no
charges in BPM models, setting a nonzero coul weight for 1-2 bonds
ensures all bonded neighbors are still included in the neighbor list
in case bonds break between neighbor list builds.
in case bonds break between neighbor list builds. If bond breakage is
disabled during a simulation run by setting the *break* keyword to *no*,
a zero coul weight for 1-2 bonds can be used to exclude bonded atoms
from the neighbor list builds
.. code-block:: LAMMPS
special_bonds lj 0 1 1 coul 0 1 1
This can be useful for post-processing, or to determine pair interaction
properties between distinct bonded particles.
To monitor the fracture of bonds in the system, all BPM bond styles
have the ability to record instances of bond breakage to output using

2
doc/src/atc_add_molecule.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC add_molecule command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> add_molecule <small|large> <tag> <group-ID>

2
doc/src/atc_add_species.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC add_species command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> add_species <tag> <group|type> <ID>

2
doc/src/atc_atom_element_map.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC atom_element_map command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> atom_element_map <eulerian|lagrangian> [<frequency>]

2
doc/src/atc_atom_weight.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC atom_weight command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> atom_weight <method> <args>

2
doc/src/atc_atomic_charge.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC atomic_charge command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> <include|omit> atomic_charge

2
doc/src/atc_boundary_dynamics.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC boundary_dynamics command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> boundary_dynamics <on|damped_harmonic|prescribed|coupled|none>

2
doc/src/atc_boundary_faceset.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC boundary_faceset command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> boundary_faceset <is|add> <faceset_name>

2
doc/src/atc_boundary_type.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC boundary type command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> boundary type <atom-type-id>

2
doc/src/atc_consistent_fe_initialization.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC consistent_fe_initialization command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> consistent_fe_initialization <on|off>

2
doc/src/atc_control_localized_lambda.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC control localized_lambda command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> control localized_lambda <on|off>

2
doc/src/atc_control_momentum.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC control momentum command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> control <physics_type> <solution_parameter> <value>
fix_modify AtC control momentum none

2
doc/src/atc_control_thermal.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC control thermal command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> control <physics_type> <solution_parameter> <value>
fix_modify <AtC fixID> control thermal <control_type> <optional_args>

2
doc/src/atc_decomposition.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC decomposition command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> decomposition <type>

2
doc/src/atc_electron_integration.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC extrinsic electron_integration command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> extrinsic electron_integration <integration_type> [<num_subcycle_steps>]

2
doc/src/atc_equilibrium_start.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC equilibrium_start command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> equilibrium_start <on|off>

2
doc/src/atc_extrinsic_exchange.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC extrinsic exchange command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> extrinsic exchange <on|off>

2
doc/src/atc_fe_md_boundary.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC fe_md_boundary command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> fe_md_boundary <faceset|interpolate|no_boundary>

2
doc/src/atc_filter_scale.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC filter scale command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> filter scale <scale>

2
doc/src/atc_filter_type.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC filter type command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> filter type <exponential|step|no_filter>

2
doc/src/atc_fix.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC fix command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> fix <field> <nodeset> <constant|function>

2
doc/src/atc_fix_flux.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC fix_flux command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> fix_flux <field> <face_set> <value|function>

2
doc/src/atc_hardy_computes.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC computes command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> computes <add|delete> <per-atom compute-ID> <volume|number>

2
doc/src/atc_hardy_fields.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC fields command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> fields <all|none>
fix_modify <AtC fixID> fields <add|delete> <list_of_fields>

2
doc/src/atc_hardy_gradients.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC gradients command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> gradients <add|delete> <list_of_fields>

2
doc/src/atc_hardy_kernel.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC kernel command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> kernel <type> <parameters>

2
doc/src/atc_hardy_on_the_fly.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC on_the_fly command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> on_the_fly <bond|kernel> <on|off>

2
doc/src/atc_hardy_rates.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC rates command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> rates <add|delete> <list_of_fields>

2
doc/src/atc_initial.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC initial command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> initial <field> <nodeset> <constant|function>

2
doc/src/atc_internal_element_set.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC internal_element_set command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> internal_element_set <element_set_name>

2
doc/src/atc_internal_quadrature.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC internal_quadrature command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> internal_quadrature <on|off> [region]

2
doc/src/atc_kernel_bandwidth.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC kernel_bandwidth command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> kernel_bandwidth <value>

2
doc/src/atc_lumped_lambda_solve.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC control lumped_lambda_solve command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> control lumped_lambda_solve <on|off>

2
doc/src/atc_mask_direction.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC control mask_direction command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> control mask_direction <direction> <on|off>

2
doc/src/atc_mass_matrix.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC mass_matrix command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> mass_matrix <fe|md_fe>

2
doc/src/atc_material.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC material command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> material <elementset_name> <material_id>

2
doc/src/atc_mesh_add_to_nodeset.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC mesh add_to_nodeset command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> mesh add_to_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

2
doc/src/atc_mesh_create.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC mesh create command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> mesh create <nx> <ny> <nz> <region-ID> <f|p> <f|p> <f|p>

2
doc/src/atc_mesh_create_elementset.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC mesh create_elementset command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> mesh create_elementset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

2
doc/src/atc_mesh_create_faceset_box.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC mesh create_faceset box command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> mesh create_faceset <id> box <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> <in|out> [units]

2
doc/src/atc_mesh_create_faceset_plane.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC mesh create_faceset plane command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> mesh create_faceset <id> plane <x|y|z> <val1> <x|y|z> <lval2> <uval2> [units]

2
doc/src/atc_mesh_create_nodeset.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC mesh create_nodeset command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> mesh create_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

2
doc/src/atc_mesh_delete_elements.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC mesh delete_elements command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> mesh delete_elements <id>

2
doc/src/atc_mesh_nodeset_to_elementset.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC mesh nodeset_to_elementset command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> mesh nodeset_to_elementset <nodeset_id> <elementset_id> <max/min>

2
doc/src/atc_mesh_output.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC mesh output command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> mesh output <file_prefix>

2
doc/src/atc_mesh_quadrature.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC mesh quadrature command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> mesh quatrature <quad>

2
doc/src/atc_mesh_read.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC mesh read command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> mesh read <f|p> <f|p> <f|p>

2
doc/src/atc_mesh_write.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC mesh write command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> mesh write <f|p> <f|p> <f|p>

2
doc/src/atc_output.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC output command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> output <filename_prefix> <frequency> [text|full_text|binary|vector_components|tensor_components]
fix_modify <AtC fixID> output index [step|time]

2
doc/src/atc_output_boundary_integral.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC output boundary_integral command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> output boundary_integral <fieldname> faceset [name]

2
doc/src/atc_output_contour_integral.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC output contour_integral command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> output contour_integral <fieldname> faceset <name> [axis [x|y|z]]

2
doc/src/atc_output_nodeset.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC output nodeset command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> output nodeset <nodeset_name> <operation>

2
doc/src/atc_output_volume_integral.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC output volume_integral command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> output volume_integral <elementset_name> <field>

2
doc/src/atc_pair_interactions.rst
View File

@ -9,7 +9,7 @@ fix_modify AtC bond_interactions command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> pair_interactions <on|off>
fix_modify <AtC fixID> bond_interactions <on|off>

2
doc/src/atc_poisson_solver.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC poisson_solver command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> poisson_solver mesh create <nx> <ny> <nz> <region-ID> <f|p> <f|p> <f|p>

2
doc/src/atc_read_restart.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC read_restart command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> read_restart <file_name>

2
doc/src/atc_remove_molecule.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC remove_molecule command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> remove_molecule <tag>

2
doc/src/atc_remove_source.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC remove_source command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> remove_source <field> <element_set>

2
doc/src/atc_remove_species.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC remove_species command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> remove_species <tag>

2
doc/src/atc_reset_atomic_reference.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC reset_atomic_reference_positions command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> reset_atomic_reference_positions

2
doc/src/atc_reset_time.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC reset_time command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> reset_time <value>

2
doc/src/atc_sample_frequency.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC sample_frequency command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> sample_frequency <freq>

2
doc/src/atc_set_reference_pe.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC set reference_potential_energy command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> set reference_potential_energy [<value|filename>]

2
doc/src/atc_source.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC source command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> source <field> <element_set> <value|function>

2
doc/src/atc_source_integration.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC source_integration command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> source_integration <fe|atom>

2
doc/src/atc_temperature_definition.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC temperature_definition command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> temperature_definition <kinetic|total>

2
doc/src/atc_time_filter.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC filter command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> filter <on|off|equilibrate>

2
doc/src/atc_time_integration.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC time_integration command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> time_integration <descriptor>

2
doc/src/atc_track_displacement.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC track_displacement command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> track_displacement <on|off>

2
doc/src/atc_unfix.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC unfix command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> unfix <field> <nodeset>

2
doc/src/atc_unfix_flux.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC unfix_flux command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> unfix_flux <field> <face_set> <value|function>

2
doc/src/atc_write_atom_weights.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC write_atom_weights command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> write_atom_weights <filename> <frequency>

2
doc/src/atc_write_restart.rst
View File

@ -6,7 +6,7 @@ fix_modify AtC write_restart command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify <AtC fixID> write_restart <file_name>

49
doc/src/bond_bpm_rotational.rst
View File

@ -10,7 +10,7 @@ Syntax
bond_style bpm/rotational keyword value attribute1 attribute2 ...
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break/no*
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break*
.. parsed-literal::
@ -80,32 +80,32 @@ respectively. Details on the calculations of shear displacements and
angular displacements can be found in :ref:`(Wang) <Wang2009>` and
:ref:`(Wang and Mora) <Wang2009b>`.
Bonds will break under sufficient stress. A breaking criteria is calculated
Bonds will break under sufficient stress. A breaking criterion is calculated
.. math::
B = \mathrm{max}\{0, \frac{f_r}{f_{r,c}} + \frac{|f_s|}{f_{s,c}} +
\frac{|\tau_b|}{\tau_{b,c}} + \frac{|\tau_t|}{\tau_{t,c}} \}
B = \mathrm{max}\left\{0, \frac{f_r}{f_{r,c}} + \frac{|f_s|}{f_{s,c}} +
\frac{|\tau_b|}{\tau_{b,c}} + \frac{|\tau_t|}{\tau_{t,c}} \right\}
where :math:`|f_s|` is the magnitude of the shear force and
:math:`|\tau_b|` and :math:`|\tau_t|` are the magnitudes of the
bending and twisting forces, respectively. The corresponding variables
bending and twisting torques, respectively. The corresponding variables
:math:`f_{r,c}` :math:`f_{s,c}`, :math:`\tau_{b,c}`, and
:math:`\tau_{t,c}` are critical limits to each force or torque. If
:math:`B` is ever equal to or exceeds one, the bond will break. This
is done by setting by setting its type to 0 such that forces and
is done by setting the bond type to 0 such that forces and
torques are no longer computed.
After computing the base magnitudes of the forces and torques, they
can be optionally multiplied by an extra factor :math:`w` to smoothly
interpolate forces and torques to zero as the bond breaks. This term
is calculated as :math:`w = (1.0 - B^4)`. This smoothing factor can be
added or removed using the *smooth* keyword.
is calculated as :math:`w = (1.0 - B^4)`. This smoothing factor can be added
or removed by setting the *smooth* keyword to *yes* or *no*, respectively.
Finally, additional damping forces and torques are applied to the two
particles. A force is applied proportional to the difference in the
normal velocity of particles using a similar construction as
dissipative particle dynamics (:ref:`(Groot) <Groot3>`):
dissipative particle dynamics :ref:`(Groot) <Groot3>`:
.. math::
@ -115,8 +115,8 @@ where :math:`\gamma_n` is the damping strength, :math:`\hat{r}` is the
radial normal vector, and :math:`\vec{v}` is the velocity difference
between the two particles. Similarly, tangential forces are applied to
each atom proportional to the relative differences in sliding
velocities with a constant prefactor :math:`\gamma_s` (:ref:`(Wang et
al.) <Wang20152>`) along with their associated torques. The rolling and
velocities with a constant prefactor :math:`\gamma_s` :ref:`(Wang et
al.) <Wang20152>` along with their associated torques. The rolling and
twisting components of the relative angular velocities of the two
atoms are also damped by applying torques with prefactors of
:math:`\gamma_r` and :math:`\gamma_t`, respectively.
@ -139,21 +139,23 @@ or :doc:`read_restart <read_restart>` commands:
* :math:`\gamma_r` (force*distance/velocity units)
* :math:`\gamma_t` (force*distance/velocity units)
However, the *normalize* option will normalize the radial and shear forces
by :math:`r_0` such that :math:`k_r` and :math:`k_s` are unit less.
If the *normalize* keyword is set to *yes*, the radial and shear forces
will be normalized by :math:`r_0` such that :math:`k_r` and :math:`k_s`
must be given in force units.
By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces using
the *overlay/pair* option. These settings require specific
Pair forces can alternatively be overlaid on top of bond forces by setting
the *overlay/pair* keyword to *yes*. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the `:doc: how to
<Howto_BPM>` page on BPMs.
restrictions. Further details can be found in the :doc:`how to
<Howto_bpm>` page on BPMs.
.. versionadded:: 28Mar2023
If the *break* option is used, then LAMMPS assumes bonds should not break
If the *break* keyword is set to *no*, LAMMPS assumes bonds should not break
during a simulation run. This will prevent some unnecessary calculation.
However, if a bond does break, it will trigger an error.
However, if a bond reaches a damage criterion greater than one,
it will trigger an error.
If the *store/local* keyword is used, an internal fix will track bonds that
break during the simulation. Whenever a bond breaks, data is processed
@ -232,16 +234,15 @@ This bond style is part of the BPM package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
By default if pair interactions are to be disabled, this bond style
requires setting
By default if pair interactions between bonded atoms are to be disabled,
this bond style requires setting
.. code-block:: LAMMPS
special_bonds lj 0 1 1 coul 1 1 1
and :doc:`newton <newton>` must be set to bond off. If the
*overlay/pair* option is used, this bond style alternatively requires
setting
and :doc:`newton <newton>` must be set to bond off. If the *overlay/pair*
keyword is set to *yes*, this bond style alternatively requires setting
.. code-block:: LAMMPS

41
doc/src/bond_bpm_spring.rst
View File

@ -10,7 +10,7 @@ Syntax
bond_style bpm/spring keyword value attribute1 attribute2 ...
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break/no*
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break*
.. parsed-literal::
@ -72,13 +72,13 @@ particles based on a model described by Clemmer and Robbins
where :math:`k` is a stiffness, :math:`r` is the current distance
and :math:`r_0` is the initial distance between the two particles, and
:math:`w` is an optional smoothing factor discussed below. Bonds will
break at a strain of :math:`\epsilon_c`. This is done by setting by
setting its type to 0 such that forces are no longer computed.
break at a strain of :math:`\epsilon_c`. This is done by setting
the bond type to 0 such that forces are no longer computed.
An additional damping force is applied to the bonded
particles. This forces is proportional to the difference in the
normal velocity of particles using a similar construction as
dissipative particle dynamics (:ref:`(Groot) <Groot4>`):
dissipative particle dynamics :ref:`(Groot) <Groot4>`:
.. math::
@ -88,9 +88,10 @@ where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
radial normal vector, and :math:`\vec{v}` is the velocity difference
between the two particles.
The smoothing factor :math:`w` can be added or removed using the
*smooth* keyword. It is constructed such that forces smoothly go
to zero, avoiding discontinuities, as bonds approach the critical strain
The smoothing factor :math:`w` can be added or removed by setting the
*smooth* keyword to *yes* or *no*, respectively. It is constructed such
that forces smoothly go to zero, avoiding discontinuities, as bonds
approach the critical strain
.. math::
@ -105,21 +106,22 @@ the data file or restart files read by the :doc:`read_data
* :math:`\epsilon_c` (unit less)
* :math:`\gamma` (force/velocity units)
However, the *normalize* option will normalize the elastic bond force by
:math:`r_0` such that :math:`k` is unit less.
If the *normalize* keyword is set to *yes*, the elastic bond force will be
normalized by :math:`r_0` such that :math:`k` must be given in force units.
By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces using
the *overlay/pair* option. These settings require specific
Pair forces can alternatively be overlaid on top of bond forces by setting
the *overlay/pair* keyword to *yes*. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the `:doc: how to
<Howto_BPM>` page on BPMs.
restrictions. Further details can be found in the :doc:`how to
<Howto_bpm>` page on BPMs.
.. versionadded:: 28Mar2023
If the *break* option is used, then LAMMPS assumes bonds should not break
If the *break* keyword is set to *no*, LAMMPS assumes bonds should not break
during a simulation run. This will prevent some unnecessary calculation.
However, if a bond does break, it will trigger an error.
However, if a bond reaches a strain greater than :math:`\epsilon_c`,
it will trigger an error.
If the *store/local* keyword is used, an internal fix will track bonds that
break during the simulation. Whenever a bond breaks, data is processed
@ -189,16 +191,15 @@ This bond style is part of the BPM package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
By default if pair interactions are to be disabled, this bond style
requires setting
By default if pair interactions between bonded atoms are to be disabled,
this bond style requires setting
.. code-block:: LAMMPS
special_bonds lj 0 1 1 coul 1 1 1
and :doc:`newton <newton>` must be set to bond off. If the
*overlay/pair* option is used, this bond style alternatively requires
setting
and :doc:`newton <newton>` must be set to bond off. If the *overlay/pair*
keyword is set to *yes*, this bond style alternatively requires setting
.. code-block:: LAMMPS

37
doc/src/compute_modify.rst
View File

@ -12,16 +12,14 @@ Syntax
* compute-ID = ID of the compute to modify
* one or more keyword/value pairs may be listed
* keyword = *extra/dof* or *extra* or *dynamic/dof* or *dynamic*
* keyword = *extra/dof* or *dynamic/dof*
.. parsed-literal::
*extra/dof* value = N
N = # of extra degrees of freedom to subtract
*extra* syntax is identical to *extra/dof*, will be disabled at some point
*dynamic/dof* value = *yes* or *no*
yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
*dynamic* syntax is identical to *dynamic/dof*, will be disabled at some point
Examples
""""""""
@ -37,19 +35,18 @@ Description
Modify one or more parameters of a previously defined compute. Not
all compute styles support all parameters.
The *extra/dof* or *extra* keyword refers to how many degrees of
freedom are subtracted (typically from :math:`3N`) as a normalizing
factor in a temperature computation. Only computes that compute a
temperature use this option. The default is 2 or 3 for :doc:`2d or 3d
systems <dimension>` which is a correction factor for an ensemble of
velocities with zero total linear momentum. For compute temp/partial,
if one or more velocity components are excluded, the value used for
*extra* is scaled accordingly. You can use a negative number for the
*extra* parameter if you need to add degrees-of-freedom. See the
:doc:`compute temp/asphere <compute_temp_asphere>` command for an
example.
The *extra/dof* keyword refers to how many degrees of freedom are
subtracted (typically from :math:`3N`) as a normalizing factor in a
temperature computation. Only computes that compute a temperature use
this option. The default is 2 or 3 for :doc:`2d or 3d systems
<dimension>` which is a correction factor for an ensemble of velocities
with zero total linear momentum. For compute temp/partial, if one or
more velocity components are excluded, the value used for *extra/dof* is
scaled accordingly. You can use a negative number for the *extra/dof*
parameter if you need to add degrees-of-freedom. See the :doc:`compute
temp/asphere <compute_temp_asphere>` command for an example.
The *dynamic/dof* or *dynamic* keyword determines whether the number
The *dynamic/dof* keyword determines whether the number
of atoms :math:`N` in the compute group and their associated degrees
of freedom (DOF) are re-computed each time a temperature is computed.
Only compute styles that calculate a temperature use this option. By
@ -61,12 +58,6 @@ are adding atoms or molecules to the system (see the :doc:`fix pour
<fix_evaporate>`), then this option should be used to ensure the
temperature is correctly normalized.
.. note::
The *extra* and *dynamic* keywords should not be used as they
are deprecated (March 2017) and will eventually be disabled. Instead,
use the equivalent *extra/dof* and *dynamic/dof* keywords.
Restrictions
""""""""""""
none
@ -79,5 +70,5 @@ Related commands
Default
"""""""
The option defaults are extra/dof = 2 or 3 for 2d or 3d systems and
dynamic/dof = *no*.
The option defaults are extra/dof = 2 or 3 for 2d or 3d systems,
respectively, and dynamic/dof = *no*.

2
doc/src/compute_property_grid.rst
View File

@ -6,7 +6,7 @@ compute property/grid command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID property/grid Nx Ny Nz input1 input2 ...

2
doc/src/compute_rdf.rst
View File

@ -202,7 +202,7 @@ change from zero to one at the location of the spike in :math:`g(r)`.
parallel efficiency and scaling. For systems, where only the type
of atoms changes (e.g., when using :doc:`fix atom/swap <fix_atom_swap>`),
you need to explicitly request the dynamic normalization updates
via :doc:`compute_modify dynamic yes <compute_modify>`
via :doc:`compute_modify dynamic/dof yes <compute_modify>`
Related commands
""""""""""""""""

2
doc/src/compute_reduce_chunk.rst
View File

@ -6,7 +6,7 @@ compute reduce/chunk command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID reduce/chunk chunkID mode input1 input2 ...

2
doc/src/compute_saed.rst
View File

@ -6,7 +6,7 @@ compute saed command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID saed lambda type1 type2 ... typeN keyword value ...

2
doc/src/compute_slice.rst
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@ -6,7 +6,7 @@ compute slice command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID slice Nstart Nstop Nskip input1 input2 ...

2
doc/src/compute_smd_contact_radius.rst
View File

@ -6,7 +6,7 @@ compute smd/contact/radius command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/contact/radius

2
doc/src/compute_smd_damage.rst
View File

@ -6,7 +6,7 @@ compute smd/damage command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/damage

2
doc/src/compute_smd_hourglass_error.rst
View File

@ -6,7 +6,7 @@ compute smd/hourglass/error command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/hourglass/error

2
doc/src/compute_smd_internal_energy.rst
View File

@ -6,7 +6,7 @@ compute smd/internal/energy command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/internal/energy

2
doc/src/compute_smd_plastic_strain.rst
View File

@ -6,7 +6,7 @@ compute smd/plastic/strain command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/plastic/strain

2
doc/src/compute_smd_plastic_strain_rate.rst
View File

@ -6,7 +6,7 @@ compute smd/plastic/strain/rate command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/plastic/strain/rate

2
doc/src/compute_smd_rho.rst
View File

@ -6,7 +6,7 @@ compute smd/rho command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/rho

2
doc/src/compute_smd_tlsph_defgrad.rst
View File

@ -6,7 +6,7 @@ compute smd/tlsph/defgrad command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/tlsph/defgrad

2
doc/src/compute_smd_tlsph_dt.rst
View File

@ -6,7 +6,7 @@ compute smd/tlsph/dt command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/tlsph/dt

2
doc/src/compute_smd_tlsph_num_neighs.rst
View File

@ -6,7 +6,7 @@ compute smd/tlsph/num/neighs command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/tlsph/num/neighs

2
doc/src/compute_smd_tlsph_shape.rst
View File

@ -6,7 +6,7 @@ compute smd/tlsph/shape command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/tlsph/shape

2
doc/src/compute_smd_tlsph_strain.rst
View File

@ -6,7 +6,7 @@ compute smd/tlsph/strain command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/tlsph/strain

2
doc/src/compute_smd_tlsph_strain_rate.rst
View File

@ -6,7 +6,7 @@ compute smd/tlsph/strain/rate command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/tlsph/strain/rate

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