Merge branch 'develop' into schererc/develop
This commit is contained in:
Axel Kohlmeyer
2
.github/workflows/codeql-analysis.yml
vendored
2
.github/workflows/codeql-analysis.yml
vendored
@ -5,6 +5,8 @@ on:
|
|||||||
push:
|
push:
|
||||||
branches: [develop]
|
branches: [develop]
|
||||||
|
|
||||||
|
workflow_dispatch:
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
analyze:
|
analyze:
|
||||||
name: Analyze
|
name: Analyze
|
||||||
|
|||||||
2
.github/workflows/compile-msvc.yml
vendored
2
.github/workflows/compile-msvc.yml
vendored
@ -5,6 +5,8 @@ on:
|
|||||||
push:
|
push:
|
||||||
branches: [develop]
|
branches: [develop]
|
||||||
|
|
||||||
|
workflow_dispatch:
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
build:
|
build:
|
||||||
name: Windows Compilation Test
|
name: Windows Compilation Test
|
||||||
|
|||||||
2
.github/workflows/unittest-macos.yml
vendored
2
.github/workflows/unittest-macos.yml
vendored
@ -5,6 +5,8 @@ on:
|
|||||||
push:
|
push:
|
||||||
branches: [develop]
|
branches: [develop]
|
||||||
|
|
||||||
|
workflow_dispatch:
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
build:
|
build:
|
||||||
name: MacOS Unit Test
|
name: MacOS Unit Test
|
||||||
|
|||||||
615
cmake/CMakeLists.jpeg
Normal file
615
cmake/CMakeLists.jpeg
Normal file
@ -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 ${USE_SETMODE}")
|
||||||
|
set(CJPEG_BMP_SOURCES rdbmp.c rdtarga.c)
|
||||||
|
set(DJPEG_BMP_SOURCES wrbmp.c wrtarga.c)
|
||||||
|
endif()
|
||||||
741
cmake/CMakeLists.png
Normal file
741
cmake/CMakeLists.png
Normal file
@ -0,0 +1,741 @@
|
|||||||
|
# CMakeLists.txt
|
||||||
|
|
||||||
|
# Copyright (C) 2018 Cosmin Truta
|
||||||
|
# Copyright (C) 2007,2009-2018 Glenn Randers-Pehrson
|
||||||
|
# Written by Christian Ehrlicher, 2007
|
||||||
|
# Revised by Roger Lowman, 2009-2010
|
||||||
|
# Revised by Clifford Yapp, 2011-2012,2017
|
||||||
|
# Revised by Roger Leigh, 2016
|
||||||
|
# Revised by Andreas Franek, 2016
|
||||||
|
# Revised by Sam Serrels, 2017
|
||||||
|
# Revised by Vadim Barkov, 2017
|
||||||
|
# Revised by Vicky Pfau, 2018
|
||||||
|
# Revised by Cameron Cawley, 2018
|
||||||
|
# Revised by Cosmin Truta, 2018
|
||||||
|
# Revised by Kyle Bentley, 2018
|
||||||
|
|
||||||
|
# This code is released under the libpng license.
|
||||||
|
# For conditions of distribution and use, see the disclaimer
|
||||||
|
# and license in png.h
|
||||||
|
|
||||||
|
cmake_minimum_required(VERSION 3.10)
|
||||||
|
cmake_policy(VERSION 3.1)
|
||||||
|
# When using CMake 3.4 and later, don't export symbols from executables unless
|
||||||
|
# the CMAKE_ENABLE_EXPORTS variable is set.
|
||||||
|
if(POLICY CMP0065)
|
||||||
|
cmake_policy(SET CMP0065 NEW)
|
||||||
|
endif()
|
||||||
|
if (POLICY CMP0077)
|
||||||
|
cmake_policy(SET CMP0077 NEW)
|
||||||
|
endif()
|
||||||
|
set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
|
||||||
|
|
||||||
|
project(libpng C ASM)
|
||||||
|
enable_testing()
|
||||||
|
|
||||||
|
set(PNGLIB_MAJOR 1)
|
||||||
|
set(PNGLIB_MINOR 6)
|
||||||
|
set(PNGLIB_RELEASE 37)
|
||||||
|
set(PNGLIB_NAME libpng${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${PNG_LIB_NAME}.cmake)
|
||||||
|
endif()
|
||||||
|
|
||||||
|
# what's with libpng-manual.txt and all the extra files?
|
||||||
|
|
||||||
|
# UNINSTALL
|
||||||
|
# do we need this?
|
||||||
|
|
||||||
|
# DIST
|
||||||
|
# do we need this?
|
||||||
|
|
||||||
|
# to create msvc import lib for mingw compiled shared lib
|
||||||
|
# pexports libpng.dll > libpng.def
|
||||||
|
# lib /def:libpng.def /machine:x86
|
||||||
@ -138,6 +138,9 @@ if(MSVC)
|
|||||||
add_compile_options(/Zc:__cplusplus)
|
add_compile_options(/Zc:__cplusplus)
|
||||||
add_compile_options(/wd4244)
|
add_compile_options(/wd4244)
|
||||||
add_compile_options(/wd4267)
|
add_compile_options(/wd4267)
|
||||||
|
if(LAMMPS_EXCEPTIONS)
|
||||||
|
add_compile_options(/EHsc)
|
||||||
|
endif()
|
||||||
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
|
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
|
|||||||
195
cmake/CMakeLists.zlib
Normal file
195
cmake/CMakeLists.zlib
Normal file
@ -0,0 +1,195 @@
|
|||||||
|
cmake_minimum_required(VERSION 3.10)
|
||||||
|
# When using CMake 3.4 and later, don't export symbols from executables unless
|
||||||
|
# the CMAKE_ENABLE_EXPORTS variable is set.
|
||||||
|
if(POLICY CMP0065)
|
||||||
|
cmake_policy(SET CMP0065 NEW)
|
||||||
|
endif()
|
||||||
|
if (POLICY CMP0077)
|
||||||
|
cmake_policy(SET CMP0077 NEW)
|
||||||
|
endif()
|
||||||
|
set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
|
||||||
|
|
||||||
|
project(zlib C)
|
||||||
|
|
||||||
|
set(VERSION "1.2.11")
|
||||||
|
|
||||||
|
option(ASM686 "Enable building i686 assembly implementation" OFF)
|
||||||
|
option(AMD64 "Enable building amd64 assembly implementation" OFF)
|
||||||
|
|
||||||
|
set(INSTALL_BIN_DIR "${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} ${ZLIB_PRIVATE_HDRS})
|
||||||
|
|
||||||
|
if(UNIX)
|
||||||
|
# On unix-like platforms the library is almost always called libz
|
||||||
|
set_target_properties(zlibstatic PROPERTIES OUTPUT_NAME z)
|
||||||
|
endif()
|
||||||
@ -8,7 +8,7 @@
|
|||||||
"installRoot": "${workspaceRoot}\\install\\${name}",
|
"installRoot": "${workspaceRoot}\\install\\${name}",
|
||||||
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
|
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
|
||||||
"buildCommandArgs": "",
|
"buildCommandArgs": "",
|
||||||
"ctestCommandArgs": "",
|
"ctestCommandArgs": "-V",
|
||||||
"inheritEnvironments": [ "msvc_x64_x64" ],
|
"inheritEnvironments": [ "msvc_x64_x64" ],
|
||||||
"variables": [
|
"variables": [
|
||||||
{
|
{
|
||||||
@ -26,11 +26,6 @@
|
|||||||
"value": "True",
|
"value": "True",
|
||||||
"type": "BOOL"
|
"type": "BOOL"
|
||||||
},
|
},
|
||||||
{
|
|
||||||
"name": "PKG_PYTHON",
|
|
||||||
"value": "True",
|
|
||||||
"type": "BOOL"
|
|
||||||
},
|
|
||||||
{
|
{
|
||||||
"name": "ENABLE_TESTING",
|
"name": "ENABLE_TESTING",
|
||||||
"value": "True",
|
"value": "True",
|
||||||
@ -46,7 +41,7 @@
|
|||||||
"installRoot": "${workspaceRoot}\\install\\${name}",
|
"installRoot": "${workspaceRoot}\\install\\${name}",
|
||||||
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
|
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
|
||||||
"buildCommandArgs": "",
|
"buildCommandArgs": "",
|
||||||
"ctestCommandArgs": "",
|
"ctestCommandArgs": "-V",
|
||||||
"inheritEnvironments": [ "msvc_x64_x64" ],
|
"inheritEnvironments": [ "msvc_x64_x64" ],
|
||||||
"variables": [
|
"variables": [
|
||||||
{
|
{
|
||||||
@ -64,11 +59,6 @@
|
|||||||
"value": "True",
|
"value": "True",
|
||||||
"type": "BOOL"
|
"type": "BOOL"
|
||||||
},
|
},
|
||||||
{
|
|
||||||
"name": "PKG_PYTHON",
|
|
||||||
"value": "True",
|
|
||||||
"type": "BOOL"
|
|
||||||
},
|
|
||||||
{
|
{
|
||||||
"name": "ENABLE_TESTING",
|
"name": "ENABLE_TESTING",
|
||||||
"value": "True",
|
"value": "True",
|
||||||
@ -102,11 +92,6 @@
|
|||||||
"value": "True",
|
"value": "True",
|
||||||
"type": "BOOL"
|
"type": "BOOL"
|
||||||
},
|
},
|
||||||
{
|
|
||||||
"name": "PKG_PYTHON",
|
|
||||||
"value": "True",
|
|
||||||
"type": "BOOL"
|
|
||||||
},
|
|
||||||
{
|
{
|
||||||
"name": "ENABLE_TESTING",
|
"name": "ENABLE_TESTING",
|
||||||
"value": "True",
|
"value": "True",
|
||||||
@ -122,7 +107,7 @@
|
|||||||
"installRoot": "${workspaceRoot}\\install\\${name}",
|
"installRoot": "${workspaceRoot}\\install\\${name}",
|
||||||
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
|
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
|
||||||
"buildCommandArgs": "",
|
"buildCommandArgs": "",
|
||||||
"ctestCommandArgs": "",
|
"ctestCommandArgs": "-V",
|
||||||
"inheritEnvironments": [ "clang_cl_x64" ],
|
"inheritEnvironments": [ "clang_cl_x64" ],
|
||||||
"variables": [
|
"variables": [
|
||||||
{
|
{
|
||||||
@ -140,11 +125,6 @@
|
|||||||
"value": "True",
|
"value": "True",
|
||||||
"type": "BOOL"
|
"type": "BOOL"
|
||||||
},
|
},
|
||||||
{
|
|
||||||
"name": "PKG_PYTHON",
|
|
||||||
"value": "True",
|
|
||||||
"type": "BOOL"
|
|
||||||
},
|
|
||||||
{
|
{
|
||||||
"name": "ENABLE_TESTING",
|
"name": "ENABLE_TESTING",
|
||||||
"value": "True",
|
"value": "True",
|
||||||
@ -158,9 +138,16 @@
|
|||||||
"configurationType": "Debug",
|
"configurationType": "Debug",
|
||||||
"buildRoot": "${workspaceRoot}\\build\\${name}",
|
"buildRoot": "${workspaceRoot}\\build\\${name}",
|
||||||
"installRoot": "${workspaceRoot}\\install\\${name}",
|
"installRoot": "${workspaceRoot}\\install\\${name}",
|
||||||
|
"buildCommandArgs": "",
|
||||||
|
"ctestCommandArgs": "-V",
|
||||||
"inheritEnvironments": [],
|
"inheritEnvironments": [],
|
||||||
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-llvm.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
|
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-llvm.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
|
||||||
"variables": [
|
"variables": [
|
||||||
|
{
|
||||||
|
"name": "PKG_ELECTRODE",
|
||||||
|
"value": "True",
|
||||||
|
"type": "BOOL"
|
||||||
|
},
|
||||||
{
|
{
|
||||||
"name": "BUILD_SHARED_LIBS",
|
"name": "BUILD_SHARED_LIBS",
|
||||||
"value": "True",
|
"value": "True",
|
||||||
@ -176,11 +163,6 @@
|
|||||||
"value": "True",
|
"value": "True",
|
||||||
"type": "BOOL"
|
"type": "BOOL"
|
||||||
},
|
},
|
||||||
{
|
|
||||||
"name": "PKG_PYTHON",
|
|
||||||
"value": "True",
|
|
||||||
"type": "BOOL"
|
|
||||||
},
|
|
||||||
{
|
{
|
||||||
"name": "ENABLE_TESTING",
|
"name": "ENABLE_TESTING",
|
||||||
"value": "True",
|
"value": "True",
|
||||||
@ -190,11 +172,6 @@
|
|||||||
"name": "FFT",
|
"name": "FFT",
|
||||||
"value": "MKL",
|
"value": "MKL",
|
||||||
"type": "STRING"
|
"type": "STRING"
|
||||||
},
|
|
||||||
{
|
|
||||||
"name": "PKG_PLUGIN",
|
|
||||||
"value": "True",
|
|
||||||
"type": "BOOL"
|
|
||||||
}
|
}
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
@ -205,8 +182,15 @@
|
|||||||
"buildRoot": "${workspaceRoot}\\build\\${name}",
|
"buildRoot": "${workspaceRoot}\\build\\${name}",
|
||||||
"installRoot": "${workspaceRoot}\\install\\${name}",
|
"installRoot": "${workspaceRoot}\\install\\${name}",
|
||||||
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-llvm.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
|
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-llvm.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
|
||||||
|
"buildCommandArgs": "",
|
||||||
|
"ctestCommandArgs": "-V",
|
||||||
"inheritEnvironments": [],
|
"inheritEnvironments": [],
|
||||||
"variables": [
|
"variables": [
|
||||||
|
{
|
||||||
|
"name": "PKG_ELECTRODE",
|
||||||
|
"value": "True",
|
||||||
|
"type": "BOOL"
|
||||||
|
},
|
||||||
{
|
{
|
||||||
"name": "BUILD_SHARED_LIBS",
|
"name": "BUILD_SHARED_LIBS",
|
||||||
"value": "True",
|
"value": "True",
|
||||||
@ -222,11 +206,6 @@
|
|||||||
"value": "True",
|
"value": "True",
|
||||||
"type": "BOOL"
|
"type": "BOOL"
|
||||||
},
|
},
|
||||||
{
|
|
||||||
"name": "PKG_PYTHON",
|
|
||||||
"value": "True",
|
|
||||||
"type": "BOOL"
|
|
||||||
},
|
|
||||||
{
|
{
|
||||||
"name": "ENABLE_TESTING",
|
"name": "ENABLE_TESTING",
|
||||||
"value": "True",
|
"value": "True",
|
||||||
@ -236,11 +215,6 @@
|
|||||||
"name": "FFT",
|
"name": "FFT",
|
||||||
"value": "MKL",
|
"value": "MKL",
|
||||||
"type": "STRING"
|
"type": "STRING"
|
||||||
},
|
|
||||||
{
|
|
||||||
"name": "PKG_PLUGIN",
|
|
||||||
"value": "True",
|
|
||||||
"type": "BOOL"
|
|
||||||
}
|
}
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
@ -251,8 +225,15 @@
|
|||||||
"buildRoot": "${workspaceRoot}\\build\\${name}",
|
"buildRoot": "${workspaceRoot}\\build\\${name}",
|
||||||
"installRoot": "${workspaceRoot}\\install\\${name}",
|
"installRoot": "${workspaceRoot}\\install\\${name}",
|
||||||
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-classic.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
|
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-classic.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
|
||||||
|
"buildCommandArgs": "",
|
||||||
|
"ctestCommandArgs": "-V",
|
||||||
"inheritEnvironments": [],
|
"inheritEnvironments": [],
|
||||||
"variables": [
|
"variables": [
|
||||||
|
{
|
||||||
|
"name": "PKG_ELECTRODE",
|
||||||
|
"value": "True",
|
||||||
|
"type": "BOOL"
|
||||||
|
},
|
||||||
{
|
{
|
||||||
"name": "BUILD_SHARED_LIBS",
|
"name": "BUILD_SHARED_LIBS",
|
||||||
"value": "True",
|
"value": "True",
|
||||||
@ -268,11 +249,6 @@
|
|||||||
"value": "True",
|
"value": "True",
|
||||||
"type": "BOOL"
|
"type": "BOOL"
|
||||||
},
|
},
|
||||||
{
|
|
||||||
"name": "PKG_PYTHON",
|
|
||||||
"value": "True",
|
|
||||||
"type": "BOOL"
|
|
||||||
},
|
|
||||||
{
|
{
|
||||||
"name": "ENABLE_TESTING",
|
"name": "ENABLE_TESTING",
|
||||||
"value": "False",
|
"value": "False",
|
||||||
@ -282,11 +258,6 @@
|
|||||||
"name": "FFT",
|
"name": "FFT",
|
||||||
"value": "MKL",
|
"value": "MKL",
|
||||||
"type": "STRING"
|
"type": "STRING"
|
||||||
},
|
|
||||||
{
|
|
||||||
"name": "PKG_PLUGIN",
|
|
||||||
"value": "True",
|
|
||||||
"type": "BOOL"
|
|
||||||
}
|
}
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
@ -297,8 +268,15 @@
|
|||||||
"buildRoot": "${workspaceRoot}\\build\\${name}",
|
"buildRoot": "${workspaceRoot}\\build\\${name}",
|
||||||
"installRoot": "${workspaceRoot}\\install\\${name}",
|
"installRoot": "${workspaceRoot}\\install\\${name}",
|
||||||
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-classic.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
|
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-classic.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
|
||||||
|
"buildCommandArgs": "",
|
||||||
|
"ctestCommandArgs": "-V",
|
||||||
"inheritEnvironments": [],
|
"inheritEnvironments": [],
|
||||||
"variables": [
|
"variables": [
|
||||||
|
{
|
||||||
|
"name": "PKG_ELECTRODE",
|
||||||
|
"value": "True",
|
||||||
|
"type": "BOOL"
|
||||||
|
},
|
||||||
{
|
{
|
||||||
"name": "BUILD_SHARED_LIBS",
|
"name": "BUILD_SHARED_LIBS",
|
||||||
"value": "True",
|
"value": "True",
|
||||||
@ -314,11 +292,6 @@
|
|||||||
"value": "True",
|
"value": "True",
|
||||||
"type": "BOOL"
|
"type": "BOOL"
|
||||||
},
|
},
|
||||||
{
|
|
||||||
"name": "PKG_PYTHON",
|
|
||||||
"value": "True",
|
|
||||||
"type": "BOOL"
|
|
||||||
},
|
|
||||||
{
|
{
|
||||||
"name": "ENABLE_TESTING",
|
"name": "ENABLE_TESTING",
|
||||||
"value": "False",
|
"value": "False",
|
||||||
@ -328,13 +301,8 @@
|
|||||||
"name": "FFT",
|
"name": "FFT",
|
||||||
"value": "MKL",
|
"value": "MKL",
|
||||||
"type": "STRING"
|
"type": "STRING"
|
||||||
},
|
|
||||||
{
|
|
||||||
"name": "PKG_PLUGIN",
|
|
||||||
"value": "True",
|
|
||||||
"type": "BOOL"
|
|
||||||
}
|
}
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
|
|||||||
@ -31,5 +31,7 @@ set(temp "${temp}const char *LAMMPS_NS::LAMMPS::git_descriptor() { return \"${te
|
|||||||
set(temp "${temp}#endif\n\n")
|
set(temp "${temp}#endif\n\n")
|
||||||
|
|
||||||
message(STATUS "Generating lmpgitversion.h...")
|
message(STATUS "Generating lmpgitversion.h...")
|
||||||
file(WRITE "${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}")
|
||||||
|
|||||||
@ -43,6 +43,7 @@ set(WIN_PACKAGES
|
|||||||
PERI
|
PERI
|
||||||
PHONON
|
PHONON
|
||||||
POEMS
|
POEMS
|
||||||
|
PLUGIN
|
||||||
PTM
|
PTM
|
||||||
QEQ
|
QEQ
|
||||||
QTB
|
QTB
|
||||||
|
|||||||
@ -13,6 +13,7 @@ VENV = $(BUILDDIR)/docenv
|
|||||||
ANCHORCHECK = $(VENV)/bin/rst_anchor_check
|
ANCHORCHECK = $(VENV)/bin/rst_anchor_check
|
||||||
SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config
|
SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config
|
||||||
MATHJAX = $(SPHINXCONFIG)/_static/mathjax
|
MATHJAX = $(SPHINXCONFIG)/_static/mathjax
|
||||||
|
MATHJAXTAG = 3.2.1
|
||||||
|
|
||||||
PYTHON = $(word 3,$(shell type python3))
|
PYTHON = $(word 3,$(shell type python3))
|
||||||
DOXYGEN = $(word 3,$(shell type doxygen))
|
DOXYGEN = $(word 3,$(shell type doxygen))
|
||||||
@ -230,12 +231,13 @@ $(VENV):
|
|||||||
$(PYTHON) -m venv $(VENV); \
|
$(PYTHON) -m venv $(VENV); \
|
||||||
. $(VENV)/bin/activate; \
|
. $(VENV)/bin/activate; \
|
||||||
pip $(PIP_OPTIONS) install --upgrade pip; \
|
pip $(PIP_OPTIONS) install --upgrade pip; \
|
||||||
|
pip $(PIP_OPTIONS) install --upgrade wheel; \
|
||||||
pip $(PIP_OPTIONS) install -r $(BUILDDIR)/utils/requirements.txt; \
|
pip $(PIP_OPTIONS) install -r $(BUILDDIR)/utils/requirements.txt; \
|
||||||
deactivate;\
|
deactivate;\
|
||||||
)
|
)
|
||||||
|
|
||||||
$(MATHJAX):
|
$(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)
|
$(ANCHORCHECK): $(VENV)
|
||||||
@( \
|
@( \
|
||||||
|
|||||||
@ -287,8 +287,8 @@ Output of JPG, PNG, and movie files
|
|||||||
|
|
||||||
The :doc:`dump image <dump_image>` command has options to output JPEG or
|
The :doc:`dump image <dump_image>` command has options to output JPEG or
|
||||||
PNG image files. Likewise the :doc:`dump movie <dump_image>` command
|
PNG image files. Likewise the :doc:`dump movie <dump_image>` command
|
||||||
outputs movie files in MPEG format. Using these options requires the
|
outputs movie files in a variety of movie formats. Using these options
|
||||||
following settings:
|
requires the following settings:
|
||||||
|
|
||||||
.. tabs::
|
.. tabs::
|
||||||
|
|
||||||
@ -328,11 +328,12 @@ following settings:
|
|||||||
JPG_LIB = -ljpeg -lpng -lz # library names
|
JPG_LIB = -ljpeg -lpng -lz # library names
|
||||||
|
|
||||||
As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
|
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
|
if make can find the graphics header and library files in their
|
||||||
specify ``JPG_LIB`` with a list of graphics libraries to include
|
default system locations. You must specify ``JPG_LIB`` with a
|
||||||
in the link. You must insure ffmpeg is in a directory where
|
list of graphics libraries to include in the link. You must make
|
||||||
LAMMPS can find it at runtime, that is a directory in your PATH
|
certain that the ffmpeg executable (or ffmpeg.exe on Windows) is
|
||||||
environment variable.
|
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
|
Using ``ffmpeg`` to output movie files requires that your machine
|
||||||
supports the "popen" function in the standard runtime library.
|
supports the "popen" function in the standard runtime library.
|
||||||
|
|||||||
@ -239,7 +239,7 @@ is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
|
|||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
3 1 27
|
3 1 19
|
||||||
4
|
4
|
||||||
1 1 4 0 0 0
|
1 1 4 0 0 0
|
||||||
-0.7071 -0.7071 0
|
-0.7071 -0.7071 0
|
||||||
|
|||||||
@ -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>`_
|
`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/>`_
|
LAMMPS developers use the `Zenodo service at CERN <https://zenodo.org/>`_
|
||||||
to create digital object identifies (DOI) for stable releases of the
|
to create digital object identifies (DOI) for stable releases of the
|
||||||
|
|||||||
@ -475,8 +475,8 @@ that package **and** the KSPACE package. See the :doc:`Build package
|
|||||||
<Build_package>` page for more info.
|
<Build_package>` page for more info.
|
||||||
|
|
||||||
For MSM, a simulation must be 3d and one can use any combination of
|
For MSM, a simulation must be 3d and one can use any combination of
|
||||||
periodic, non-periodic, or shrink-wrapped boundaries (specified using
|
periodic, non-periodic, but not shrink-wrapped boundaries (specified
|
||||||
the :doc:`boundary <boundary>` command).
|
using the :doc:`boundary <boundary>` command).
|
||||||
|
|
||||||
For Ewald and PPPM, a simulation must be 3d and periodic in all
|
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
|
dimensions. The only exception is if the slab option is set with
|
||||||
|
|||||||
@ -4,7 +4,7 @@ min_style cg command
|
|||||||
====================
|
====================
|
||||||
|
|
||||||
min_style hftn command
|
min_style hftn command
|
||||||
====================
|
======================
|
||||||
|
|
||||||
min_style sd command
|
min_style sd command
|
||||||
====================
|
====================
|
||||||
|
|||||||
@ -20,28 +20,37 @@ Examples
|
|||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
|
|
||||||
Using a pair style of none means pair forces and energies are not
|
Using a pair style of *none* means that any previous pair style setting
|
||||||
computed.
|
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
|
As a consequence there will be a pairwise force cutoff of 0.0, which has
|
||||||
within the neighbor skin distance (see the :doc:`neighbor <neighbor>`
|
implications for the default setting of the neighbor list and the
|
||||||
command) are communicated between processors. You must insure the
|
communication cutoff. Those are the sum of the largest pairwise cutoff
|
||||||
skin distance is large enough to acquire atoms needed for computing
|
and the neighbor skin distance (see the documentation of the
|
||||||
bonds, angles, etc.
|
: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
|
A pair style of *none* will also not request a pairwise neighbor list.
|
||||||
being built. However if the :doc:`neighbor <neighbor>` style is *bin*,
|
However if the :doc:`neighbor <neighbor>` style is *bin*, data
|
||||||
data structures for binning are still allocated. If the neighbor skin
|
structures for binning are still allocated. If the neighbor list cutoff
|
||||||
distance is small, then these data structures can consume a large
|
is small, then these data structures can consume a large amount of
|
||||||
amount of memory. So you should either set the neighbor style to
|
memory. So you should either set the neighbor style to *nsq* or set the
|
||||||
*nsq* or set the skin distance to a larger value.
|
skin distance to a larger value.
|
||||||
|
|
||||||
See the :doc:`pair_style zero <pair_zero>` for a way to trigger the
|
See the :doc:`pair_style zero <pair_zero>` for a way to set a pairwise
|
||||||
building of a neighbor lists, but compute no pairwise interactions.
|
cutoff and thus trigger the building of a neighbor lists and setting
|
||||||
|
a corresponding communication cutoff, but compute no pairwise interactions.
|
||||||
|
|
||||||
Restrictions
|
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
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|||||||
@ -6,4 +6,3 @@ breathe
|
|||||||
Pygments
|
Pygments
|
||||||
six
|
six
|
||||||
pyyaml
|
pyyaml
|
||||||
wheel
|
|
||||||
|
|||||||
@ -1324,6 +1324,7 @@ hexatic
|
|||||||
hexorder
|
hexorder
|
||||||
Heyes
|
Heyes
|
||||||
HfO
|
HfO
|
||||||
|
hftn
|
||||||
hgrid
|
hgrid
|
||||||
hhmrr
|
hhmrr
|
||||||
Hibbs
|
Hibbs
|
||||||
@ -2804,6 +2805,7 @@ quatk
|
|||||||
quatw
|
quatw
|
||||||
queryargs
|
queryargs
|
||||||
Queteschiner
|
Queteschiner
|
||||||
|
quickmin
|
||||||
qw
|
qw
|
||||||
qx
|
qx
|
||||||
qy
|
qy
|
||||||
@ -3058,6 +3060,7 @@ screenshot
|
|||||||
screenshots
|
screenshots
|
||||||
Scripps
|
Scripps
|
||||||
Scripta
|
Scripta
|
||||||
|
sd
|
||||||
sdk
|
sdk
|
||||||
sdpd
|
sdpd
|
||||||
SDPD
|
SDPD
|
||||||
|
|||||||
@ -62,10 +62,10 @@ shutil.copy(args.lib,'lammps')
|
|||||||
# create a virtual environment for building the wheel
|
# create a virtual environment for building the wheel
|
||||||
shutil.rmtree('buildwheel',True)
|
shutil.rmtree('buildwheel',True)
|
||||||
try:
|
try:
|
||||||
txt = subprocess.check_output([sys.executable, '-m', 'virtualenv', 'buildwheel', '-p', sys.executable], stderr=subprocess.STDOUT, shell=False)
|
txt = subprocess.check_output([sys.executable, '-m', 'venv', 'buildwheel'], stderr=subprocess.STDOUT, shell=False)
|
||||||
print(txt.decode('UTF-8'))
|
print(txt.decode('UTF-8'))
|
||||||
except subprocess.CalledProcessError as err:
|
except subprocess.CalledProcessError as err:
|
||||||
sys.exit("Failed to create a virtualenv: {0}".format(err.output.decode('UTF-8')))
|
sys.exit("Failed to create a virtual environment: {0}".format(err.output.decode('UTF-8')))
|
||||||
|
|
||||||
# now run the commands to build the wheel. those must be in a separate script
|
# now run the commands to build the wheel. those must be in a separate script
|
||||||
# and run in subprocess, since this will use the virtual environment and
|
# and run in subprocess, since this will use the virtual environment and
|
||||||
|
|||||||
@ -58,6 +58,9 @@ PPPMDielectric::PPPMDielectric(LAMMPS *_lmp) : PPPM(_lmp)
|
|||||||
phi = nullptr;
|
phi = nullptr;
|
||||||
potflag = 0;
|
potflag = 0;
|
||||||
|
|
||||||
|
// no warnings about non-neutral systems from qsum_qsq()
|
||||||
|
warn_nonneutral = 2;
|
||||||
|
|
||||||
avec = dynamic_cast<AtomVecDielectric *>( atom->style_match("dielectric"));
|
avec = dynamic_cast<AtomVecDielectric *>( atom->style_match("dielectric"));
|
||||||
if (!avec) error->all(FLERR,"pppm/dielectric requires atom style dielectric");
|
if (!avec) error->all(FLERR,"pppm/dielectric requires atom style dielectric");
|
||||||
}
|
}
|
||||||
@ -463,25 +466,3 @@ void PPPMDielectric::slabcorr()
|
|||||||
efield[i][2] += ffact * eps[i]*(dipole_all - qsum*x[i][2]);
|
efield[i][2] += ffact * eps[i]*(dipole_all - qsum*x[i][2]);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
compute qsum,qsqsum,q2 and ignore error/warning if not charge neutral
|
|
||||||
called whenever charges are changed
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void PPPMDielectric::qsum_qsq()
|
|
||||||
{
|
|
||||||
const double * const q = atom->q;
|
|
||||||
const int nlocal = atom->nlocal;
|
|
||||||
double qsum_local(0.0), qsqsum_local(0.0);
|
|
||||||
|
|
||||||
for (int i = 0; i < nlocal; i++) {
|
|
||||||
qsum_local += q[i];
|
|
||||||
qsqsum_local += q[i]*q[i];
|
|
||||||
}
|
|
||||||
|
|
||||||
MPI_Allreduce(&qsum_local,&qsum,1,MPI_DOUBLE,MPI_SUM,world);
|
|
||||||
MPI_Allreduce(&qsqsum_local,&qsqsum,1,MPI_DOUBLE,MPI_SUM,world);
|
|
||||||
|
|
||||||
q2 = qsqsum * force->qqrd2e;
|
|
||||||
}
|
|
||||||
|
|||||||
@ -34,8 +34,6 @@ class PPPMDielectric : public PPPM {
|
|||||||
double *phi;
|
double *phi;
|
||||||
int potflag; // 1/0 if per-atom electrostatic potential phi is needed
|
int potflag; // 1/0 if per-atom electrostatic potential phi is needed
|
||||||
|
|
||||||
void qsum_qsq();
|
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
void slabcorr() override;
|
void slabcorr() override;
|
||||||
|
|
||||||
|
|||||||
@ -65,6 +65,9 @@ PPPMDispDielectric::PPPMDispDielectric(LAMMPS *_lmp) : PPPMDisp(_lmp)
|
|||||||
|
|
||||||
mu_flag = 0;
|
mu_flag = 0;
|
||||||
|
|
||||||
|
// no warnings about non-neutral systems from qsum_qsq()
|
||||||
|
warn_nonneutral = 2;
|
||||||
|
|
||||||
efield = nullptr;
|
efield = nullptr;
|
||||||
phi = nullptr;
|
phi = nullptr;
|
||||||
potflag = 0;
|
potflag = 0;
|
||||||
@ -837,25 +840,3 @@ double PPPMDispDielectric::memory_usage()
|
|||||||
bytes += nmax * sizeof(double);
|
bytes += nmax * sizeof(double);
|
||||||
return bytes;
|
return bytes;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
compute qsum,qsqsum,q2 and give error/warning if not charge neutral
|
|
||||||
called initially, when particle count changes, when charges are changed
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void PPPMDispDielectric::qsum_qsq()
|
|
||||||
{
|
|
||||||
const double * const q = atom->q;
|
|
||||||
const int nlocal = atom->nlocal;
|
|
||||||
double qsum_local(0.0), qsqsum_local(0.0);
|
|
||||||
|
|
||||||
for (int i = 0; i < nlocal; i++) {
|
|
||||||
qsum_local += q[i];
|
|
||||||
qsqsum_local += q[i]*q[i];
|
|
||||||
}
|
|
||||||
|
|
||||||
MPI_Allreduce(&qsum_local,&qsum,1,MPI_DOUBLE,MPI_SUM,world);
|
|
||||||
MPI_Allreduce(&qsqsum_local,&qsqsum,1,MPI_DOUBLE,MPI_SUM,world);
|
|
||||||
|
|
||||||
q2 = qsqsum * force->qqrd2e;
|
|
||||||
}
|
|
||||||
|
|||||||
@ -30,8 +30,7 @@ class PPPMDispDielectric : public PPPMDisp {
|
|||||||
~PPPMDispDielectric() override;
|
~PPPMDispDielectric() override;
|
||||||
double memory_usage() override;
|
double memory_usage() override;
|
||||||
void compute(int, int) override;
|
void compute(int, int) override;
|
||||||
void qsum_qsq();
|
void slabcorr(int) override;
|
||||||
void slabcorr(int);
|
|
||||||
|
|
||||||
double **efield;
|
double **efield;
|
||||||
double *phi;
|
double *phi;
|
||||||
|
|||||||
@ -95,6 +95,7 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp)
|
|||||||
pairParameters = nullptr;
|
pairParameters = nullptr;
|
||||||
tripletParameters = nullptr;
|
tripletParameters = nullptr;
|
||||||
bop_elements = nullptr;
|
bop_elements = nullptr;
|
||||||
|
bop_masses = nullptr;
|
||||||
bop_types = 0;
|
bop_types = 0;
|
||||||
|
|
||||||
pairlist1 = nullptr;
|
pairlist1 = nullptr;
|
||||||
@ -183,17 +184,13 @@ PairBOP::~PairBOP()
|
|||||||
if (bop_elements)
|
if (bop_elements)
|
||||||
for (int i = 0; i < bop_types; i++) delete[] bop_elements[i];
|
for (int i = 0; i < bop_types; i++) delete[] bop_elements[i];
|
||||||
delete[] bop_elements;
|
delete[] bop_elements;
|
||||||
|
delete[] bop_masses;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void PairBOP::compute(int eflag, int vflag)
|
void PairBOP::compute(int eflag, int vflag)
|
||||||
{
|
{
|
||||||
double minbox = MIN(MIN(domain->xprd, domain->yprd), domain->zprd);
|
|
||||||
if (minbox-0.001 < 6.0*cutmax)
|
|
||||||
error->all(FLERR,"Pair style bop requires system dimension "
|
|
||||||
"of at least {:.4}",6.0*cutmax);
|
|
||||||
|
|
||||||
int i, ii, j, jj;
|
int i, ii, j, jj;
|
||||||
int nlisti, *ilist;
|
int nlisti, *ilist;
|
||||||
tagint i_tag,j_tag, itype, jtype;
|
tagint i_tag,j_tag, itype, jtype;
|
||||||
@ -203,6 +200,7 @@ void PairBOP::compute(int eflag, int vflag)
|
|||||||
|
|
||||||
int newton_pair = force->newton_pair;
|
int newton_pair = force->newton_pair;
|
||||||
int nlocal = atom->nlocal;
|
int nlocal = atom->nlocal;
|
||||||
|
double **x = atom->x;
|
||||||
double **f = atom->f;
|
double **f = atom->f;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
tagint *tag = atom->tag;
|
tagint *tag = atom->tag;
|
||||||
@ -226,7 +224,15 @@ void PairBOP::compute(int eflag, int vflag)
|
|||||||
temp_ij = BOP_index[i] + jj;
|
temp_ij = BOP_index[i] + jj;
|
||||||
j = ilist[neigh_index[temp_ij]];
|
j = ilist[neigh_index[temp_ij]];
|
||||||
j_tag = tag[j];
|
j_tag = tag[j];
|
||||||
if (j_tag <= i_tag) continue;
|
if (i_tag > j_tag) {
|
||||||
|
if ((i_tag+j_tag) % 2 == 0) continue;
|
||||||
|
} else if (i_tag < j_tag) {
|
||||||
|
if ((i_tag+j_tag) % 2 == 1) continue;
|
||||||
|
} else {
|
||||||
|
if (x[j][2] < x[i][2]) continue;
|
||||||
|
if (x[j][2] == x[i][2] && x[j][1] < x[i][1]) continue;
|
||||||
|
if (x[j][2] == x[i][2] && x[j][1] == x[i][1] && x[j][0] < x[i][0]) continue;
|
||||||
|
}
|
||||||
jtype = map[type[j]];
|
jtype = map[type[j]];
|
||||||
int param_ij = elem2param[itype][jtype];
|
int param_ij = elem2param[itype][jtype];
|
||||||
sigB_0 = SigmaBo(ii,jj);
|
sigB_0 = SigmaBo(ii,jj);
|
||||||
@ -256,7 +262,15 @@ void PairBOP::compute(int eflag, int vflag)
|
|||||||
temp_ij = BOP_index2[i] + jj;
|
temp_ij = BOP_index2[i] + jj;
|
||||||
j = ilist[neigh_index2[temp_ij]];
|
j = ilist[neigh_index2[temp_ij]];
|
||||||
j_tag = tag[j];
|
j_tag = tag[j];
|
||||||
if (j_tag <= i_tag) continue;
|
if (i_tag > j_tag) {
|
||||||
|
if ((i_tag+j_tag) % 2 == 0) continue;
|
||||||
|
} else if (i_tag < j_tag) {
|
||||||
|
if ((i_tag+j_tag) % 2 == 1) continue;
|
||||||
|
} else {
|
||||||
|
if (x[j][2] < x[i][2]) continue;
|
||||||
|
if (x[j][2] == x[i][2] && x[j][1] < x[i][1]) continue;
|
||||||
|
if (x[j][2] == x[i][2] && x[j][1] == x[i][1] && x[j][0] < x[i][0]) continue;
|
||||||
|
}
|
||||||
PairList2 & p2_ij = pairlist2[temp_ij];
|
PairList2 & p2_ij = pairlist2[temp_ij];
|
||||||
dpr2 = -p2_ij.dRep / p2_ij.r;
|
dpr2 = -p2_ij.dRep / p2_ij.r;
|
||||||
ftmp1 = dpr2 * p2_ij.dis[0];
|
ftmp1 = dpr2 * p2_ij.dis[0];
|
||||||
@ -349,16 +363,16 @@ void PairBOP::settings(int narg, char **arg)
|
|||||||
|
|
||||||
void PairBOP::coeff(int narg, char **arg)
|
void PairBOP::coeff(int narg, char **arg)
|
||||||
{
|
{
|
||||||
const int n = atom->ntypes;
|
const int np1 = atom->ntypes+1;
|
||||||
delete [] map;
|
delete[] map;
|
||||||
map = new int[n+1];
|
map = new int[np1];
|
||||||
memory->destroy(setflag);
|
memory->destroy(setflag);
|
||||||
memory->destroy(cutsq);
|
memory->destroy(cutsq);
|
||||||
memory->destroy(cutghost);
|
memory->destroy(cutghost);
|
||||||
memory->create(setflag,n+1,n+1,"BOP:setflag");
|
memory->create(setflag,np1,np1,"BOP:setflag");
|
||||||
memory->create(cutsq,n+1,n+1,"BOP:cutsq");
|
memory->create(cutsq,np1,np1,"BOP:cutsq");
|
||||||
memory->create(cutghost,n+1,n+1,"BOP:cutghost");
|
memory->create(cutghost,np1,np1,"BOP:cutghost");
|
||||||
bytes = (n+1)*(n+1) * (sizeof (int) + 2.0*sizeof (double));
|
bytes = np1*np1*(sizeof (int) + 2.0*sizeof (double));
|
||||||
|
|
||||||
map_element2type(narg-3, arg+3);
|
map_element2type(narg-3, arg+3);
|
||||||
|
|
||||||
@ -370,22 +384,23 @@ void PairBOP::coeff(int narg, char **arg)
|
|||||||
// and check for missing elements
|
// and check for missing elements
|
||||||
|
|
||||||
if (comm->me == 0) {
|
if (comm->me == 0) {
|
||||||
for (int i = 1; i <= n; i++) {
|
for (int i = 1; i < np1; i++) {
|
||||||
int j;
|
int j;
|
||||||
if (map[i] >= 0) {
|
if (map[i] >= 0) {
|
||||||
for (j = 0; j < bop_types; j++) {
|
for (j = 0; j < bop_types; j++) {
|
||||||
if (strcmp(elements[map[i]],bop_elements[j]) == 0) {
|
if (strcmp(elements[map[i]], bop_elements[j]) == 0) {
|
||||||
map[i] = j;
|
map[i] = j;
|
||||||
|
atom->set_mass(FLERR, i, bop_masses[j]);
|
||||||
break;
|
break;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
if (j == bop_types)
|
if (j == bop_types)
|
||||||
error->one(FLERR,"Element {} not found in bop potential file {}",
|
error->one(FLERR,"Element {} not found in bop potential file {}",
|
||||||
elements[map[i]],arg[2]);
|
elements[map[i]], arg[2]);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
MPI_Bcast(map,atom->ntypes+1,MPI_INT,0,world);
|
MPI_Bcast(map,np1,MPI_INT,0,world);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -1849,9 +1864,10 @@ void PairBOP::read_table(char *filename)
|
|||||||
PotentialFileReader *reader = nullptr;
|
PotentialFileReader *reader = nullptr;
|
||||||
|
|
||||||
if (bop_elements) {
|
if (bop_elements) {
|
||||||
for (int i = 0; i < bop_types; i++) delete [] bop_elements[i];
|
for (int i = 0; i < bop_types; i++) delete[] bop_elements[i];
|
||||||
delete [] bop_elements;
|
delete[] bop_elements;
|
||||||
}
|
}
|
||||||
|
delete[] bop_masses;
|
||||||
|
|
||||||
if (comm->me == 0) {
|
if (comm->me == 0) {
|
||||||
try {
|
try {
|
||||||
@ -1862,10 +1878,11 @@ void PairBOP::read_table(char *filename)
|
|||||||
"elements",bop_types));
|
"elements",bop_types));
|
||||||
|
|
||||||
bop_elements = new char*[bop_types];
|
bop_elements = new char*[bop_types];
|
||||||
|
bop_masses = new double[bop_types];
|
||||||
for (int i=0; i < bop_types; ++i) {
|
for (int i=0; i < bop_types; ++i) {
|
||||||
ValueTokenizer values = reader->next_values(3);
|
ValueTokenizer values = reader->next_values(3);
|
||||||
values.next_int(); // element number in PTE (ignored)
|
values.next_int(); // element number (ignored)
|
||||||
values.next_double(); // element mass (ignored)
|
bop_masses[i] = values.next_double(); // element mass
|
||||||
bop_elements[i] = utils::strdup(values.next_string());
|
bop_elements[i] = utils::strdup(values.next_string());
|
||||||
}
|
}
|
||||||
} catch (TokenizerException &e) {
|
} catch (TokenizerException &e) {
|
||||||
@ -1878,8 +1895,12 @@ void PairBOP::read_table(char *filename)
|
|||||||
allocate();
|
allocate();
|
||||||
memory->create(rcut,npairs,"BOP:rcut");
|
memory->create(rcut,npairs,"BOP:rcut");
|
||||||
|
|
||||||
// copy element labels to all MPI ranks for use with write_tables()
|
// copy element labels and masses to all MPI ranks for use with
|
||||||
if (comm->me != 0) bop_elements = new char*[bop_types];
|
// write_tables() and to set the per-type masses
|
||||||
|
if (comm->me != 0) {
|
||||||
|
bop_elements = new char*[bop_types];
|
||||||
|
bop_masses = new double[bop_types];
|
||||||
|
}
|
||||||
for (int i = 0; i < bop_types; ++i) {
|
for (int i = 0; i < bop_types; ++i) {
|
||||||
int n=0;
|
int n=0;
|
||||||
if (comm->me == 0) n = strlen(bop_elements[i])+1;
|
if (comm->me == 0) n = strlen(bop_elements[i])+1;
|
||||||
@ -1887,6 +1908,7 @@ void PairBOP::read_table(char *filename)
|
|||||||
if (comm->me != 0) bop_elements[i] = new char[n];
|
if (comm->me != 0) bop_elements[i] = new char[n];
|
||||||
MPI_Bcast(bop_elements[i],n,MPI_CHAR,0,world);
|
MPI_Bcast(bop_elements[i],n,MPI_CHAR,0,world);
|
||||||
}
|
}
|
||||||
|
MPI_Bcast(bop_masses, bop_types, MPI_DOUBLE, 0, world);
|
||||||
|
|
||||||
if (comm->me == 0) {
|
if (comm->me == 0) {
|
||||||
try {
|
try {
|
||||||
@ -2015,7 +2037,7 @@ void PairBOP::read_table(char *filename)
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
delete [] singletable;
|
delete[] singletable;
|
||||||
|
|
||||||
singletable = new double[nr];
|
singletable = new double[nr];
|
||||||
for (int i = 0; i < npairs; i++) {
|
for (int i = 0; i < npairs; i++) {
|
||||||
@ -2043,7 +2065,7 @@ void PairBOP::read_table(char *filename)
|
|||||||
p.betaP = new TabularFunction();
|
p.betaP = new TabularFunction();
|
||||||
(p.betaP)->set_values(nr, 0.0, rcut[i], singletable);
|
(p.betaP)->set_values(nr, 0.0, rcut[i], singletable);
|
||||||
}
|
}
|
||||||
delete [] singletable;
|
delete[] singletable;
|
||||||
|
|
||||||
singletable = new double[nBOt];
|
singletable = new double[nBOt];
|
||||||
for (int i = 0; i < npairs; i++) {
|
for (int i = 0; i < npairs; i++) {
|
||||||
@ -2053,7 +2075,7 @@ void PairBOP::read_table(char *filename)
|
|||||||
p.bo = new TabularFunction();
|
p.bo = new TabularFunction();
|
||||||
(p.bo)->set_values(nBOt, 0.0, 1.0, singletable);
|
(p.bo)->set_values(nBOt, 0.0, 1.0, singletable);
|
||||||
}
|
}
|
||||||
delete [] singletable;
|
delete[] singletable;
|
||||||
|
|
||||||
nbuf = 0;
|
nbuf = 0;
|
||||||
for (int i = 0; i < bop_types; i++) {
|
for (int i = 0; i < bop_types; i++) {
|
||||||
@ -2107,7 +2129,7 @@ void PairBOP::read_table(char *filename)
|
|||||||
(p.cphi)->set_values(nr, 0.0, rcut[i], singletable);
|
(p.cphi)->set_values(nr, 0.0, rcut[i], singletable);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
delete [] singletable;
|
delete[] singletable;
|
||||||
}
|
}
|
||||||
|
|
||||||
memory->destroy(rcut);
|
memory->destroy(rcut);
|
||||||
|
|||||||
@ -109,6 +109,7 @@ class PairBOP : public Pair {
|
|||||||
int npairs; // number of element pairs
|
int npairs; // number of element pairs
|
||||||
int ntriples; // number of all triples
|
int ntriples; // number of all triples
|
||||||
char **bop_elements; // names of elements in potential file
|
char **bop_elements; // names of elements in potential file
|
||||||
|
double *bop_masses; // masses of elements in potential file
|
||||||
double bytes;
|
double bytes;
|
||||||
|
|
||||||
int otfly; // = 1 faster, more memory, = 0 slower, less memory
|
int otfly; // = 1 faster, more memory, = 0 slower, less memory
|
||||||
|
|||||||
@ -402,26 +402,20 @@ void AngleTable::read_table(Table *tb, char *file, char *keyword)
|
|||||||
|
|
||||||
// read a,e,f table values from file
|
// read a,e,f table values from file
|
||||||
|
|
||||||
int cerror = 0;
|
|
||||||
reader.skip_line();
|
reader.skip_line();
|
||||||
for (int i = 0; i < tb->ninput; i++) {
|
for (int i = 0; i < tb->ninput; i++) {
|
||||||
line = reader.next_line(4);
|
line = reader.next_line();
|
||||||
try {
|
try {
|
||||||
ValueTokenizer values(line);
|
ValueTokenizer values(line);
|
||||||
values.next_int();
|
values.next_int();
|
||||||
tb->afile[i] = values.next_double();
|
tb->afile[i] = values.next_double();
|
||||||
tb->efile[i] = values.next_double();
|
tb->efile[i] = values.next_double();
|
||||||
tb->ffile[i] = values.next_double();
|
tb->ffile[i] = values.next_double();
|
||||||
} catch (TokenizerException &) {
|
} catch (TokenizerException &e) {
|
||||||
++cerror;
|
error->one(FLERR, "Error parsing angle table '{}' line {} of {}. {}\nLine was: {}", keyword,
|
||||||
|
i + 1, tb->ninput, e.what(), line);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
// warn if data was read incompletely, e.g. columns were missing
|
|
||||||
|
|
||||||
if (cerror)
|
|
||||||
error->warning(FLERR, "{} of {} lines in table incomplete or could not be parsed", cerror,
|
|
||||||
tb->ninput);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
|
|||||||
@ -325,20 +325,20 @@ void BondTable::read_table(Table *tb, char *file, char *keyword)
|
|||||||
|
|
||||||
// read r,e,f table values from file
|
// read r,e,f table values from file
|
||||||
|
|
||||||
int cerror = 0;
|
|
||||||
int r0idx = -1;
|
int r0idx = -1;
|
||||||
|
|
||||||
reader.skip_line();
|
reader.skip_line();
|
||||||
for (int i = 0; i < tb->ninput; i++) {
|
for (int i = 0; i < tb->ninput; i++) {
|
||||||
line = reader.next_line(4);
|
line = reader.next_line();
|
||||||
try {
|
try {
|
||||||
ValueTokenizer values(line);
|
ValueTokenizer values(line);
|
||||||
values.next_int();
|
values.next_int();
|
||||||
tb->rfile[i] = values.next_double();
|
tb->rfile[i] = values.next_double();
|
||||||
tb->efile[i] = values.next_double();
|
tb->efile[i] = values.next_double();
|
||||||
tb->ffile[i] = values.next_double();
|
tb->ffile[i] = values.next_double();
|
||||||
} catch (TokenizerException &) {
|
} catch (TokenizerException &e) {
|
||||||
++cerror;
|
error->one(FLERR, "Error parsing bond table '{}' line {} of {}. {}\nLine was: {}", keyword,
|
||||||
|
i + 1, tb->ninput, e.what(), line);
|
||||||
}
|
}
|
||||||
|
|
||||||
if (tb->efile[i] < emin) {
|
if (tb->efile[i] < emin) {
|
||||||
@ -373,21 +373,11 @@ void BondTable::read_table(Table *tb, char *file, char *keyword)
|
|||||||
if (f > fleft && f > fright) ferror++;
|
if (f > fleft && f > fright) ferror++;
|
||||||
}
|
}
|
||||||
|
|
||||||
if (ferror) {
|
if (ferror)
|
||||||
error->warning(FLERR,
|
error->warning(FLERR,
|
||||||
"{} of {} force values in table are inconsistent with -dE/dr.\n"
|
"{} of {} force values in table are inconsistent with -dE/dr.\n"
|
||||||
"WARNING: Should only be flagged at inflection points",
|
"WARNING: Should only be flagged at inflection points",
|
||||||
ferror, tb->ninput);
|
ferror, tb->ninput);
|
||||||
}
|
|
||||||
|
|
||||||
// warn if data was read incompletely, e.g. columns were missing
|
|
||||||
|
|
||||||
if (cerror) {
|
|
||||||
error->warning(FLERR,
|
|
||||||
"{} of {} lines in table were incomplete or could not be"
|
|
||||||
" parsed completely",
|
|
||||||
cerror, tb->ninput);
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
|
|||||||
@ -1020,23 +1020,24 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword)
|
|||||||
// read a,e,f table values from file
|
// read a,e,f table values from file
|
||||||
|
|
||||||
for (int i = 0; i < tb->ninput; i++) {
|
for (int i = 0; i < tb->ninput; i++) {
|
||||||
|
line = reader.next_line();
|
||||||
try {
|
try {
|
||||||
|
ValueTokenizer values(line);
|
||||||
if (tb->f_unspecified) {
|
if (tb->f_unspecified) {
|
||||||
ValueTokenizer values = reader.next_values(3);
|
|
||||||
values.next_int();
|
values.next_int();
|
||||||
tb->phifile[i] = values.next_double();
|
tb->phifile[i] = values.next_double();
|
||||||
tb->efile[i] = values.next_double();
|
tb->efile[i] = values.next_double();
|
||||||
} else {
|
} else {
|
||||||
ValueTokenizer values = reader.next_values(4);
|
|
||||||
values.next_int();
|
values.next_int();
|
||||||
tb->phifile[i] = values.next_double();
|
tb->phifile[i] = values.next_double();
|
||||||
tb->efile[i] = values.next_double();
|
tb->efile[i] = values.next_double();
|
||||||
tb->ffile[i] = values.next_double();
|
tb->ffile[i] = values.next_double();
|
||||||
}
|
}
|
||||||
} catch (TokenizerException &e) {
|
} catch (TokenizerException &e) {
|
||||||
error->one(FLERR, e.what());
|
error->one(FLERR, "Error parsing dihedral table '{}' line {} of {}. {}\nLine was: {}",
|
||||||
|
keyword, i + 1, tb->ninput, e.what(), line);
|
||||||
}
|
}
|
||||||
} //for (int i = 0; (i < tb->ninput) && fp; i++) {
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
|
|||||||
@ -52,6 +52,11 @@ namespace ReaxFF {
|
|||||||
sin_jkl = sin(p_jkl->theta);
|
sin_jkl = sin(p_jkl->theta);
|
||||||
cos_jkl = cos(p_jkl->theta);
|
cos_jkl = cos(p_jkl->theta);
|
||||||
|
|
||||||
|
if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) sin_ijk = MIN_SINE;
|
||||||
|
else if (sin_ijk <= 0 && sin_ijk >= -MIN_SINE) sin_ijk = -MIN_SINE;
|
||||||
|
if (sin_jkl >= 0 && sin_jkl <= MIN_SINE) sin_jkl = MIN_SINE;
|
||||||
|
else if (sin_jkl <= 0 && sin_jkl >= -MIN_SINE) sin_jkl = -MIN_SINE;
|
||||||
|
|
||||||
/* omega */
|
/* omega */
|
||||||
unnorm_cos_omega = -rvec_Dot(dvec_ij, dvec_jk) * rvec_Dot(dvec_jk, dvec_kl) +
|
unnorm_cos_omega = -rvec_Dot(dvec_ij, dvec_jk) * rvec_Dot(dvec_jk, dvec_kl) +
|
||||||
SQR(r_jk) * rvec_Dot(dvec_ij, dvec_kl);
|
SQR(r_jk) * rvec_Dot(dvec_ij, dvec_kl);
|
||||||
@ -71,22 +76,16 @@ namespace ReaxFF {
|
|||||||
hnhd = r_ij * r_kl * cos_ijk * sin_jkl;
|
hnhd = r_ij * r_kl * cos_ijk * sin_jkl;
|
||||||
hnhe = r_ij * r_kl * sin_ijk * cos_jkl;
|
hnhe = r_ij * r_kl * sin_ijk * cos_jkl;
|
||||||
|
|
||||||
poem = 2.0 * r_ij * r_kl * sin_ijk * sin_jkl;
|
|
||||||
if (poem < 1e-20) poem = 1e-20;
|
|
||||||
|
|
||||||
tel = SQR(r_ij) + SQR(r_jk) + SQR(r_kl) - SQR(r_li) -
|
tel = SQR(r_ij) + SQR(r_jk) + SQR(r_kl) - SQR(r_li) -
|
||||||
2.0 * (r_ij * r_jk * cos_ijk - r_ij * r_kl * cos_ijk * cos_jkl +
|
2.0 * (r_ij * r_jk * cos_ijk - r_ij * r_kl * cos_ijk * cos_jkl +
|
||||||
r_jk * r_kl * cos_jkl);
|
r_jk * r_kl * cos_jkl);
|
||||||
|
|
||||||
|
poem = 2.0 * r_ij * r_kl * sin_ijk * sin_jkl;
|
||||||
|
|
||||||
arg = tel / poem;
|
arg = tel / poem;
|
||||||
if (arg > 1.0) arg = 1.0;
|
if (arg > 1.0) arg = 1.0;
|
||||||
if (arg < -1.0) arg = -1.0;
|
if (arg < -1.0) arg = -1.0;
|
||||||
|
|
||||||
if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) sin_ijk = MIN_SINE;
|
|
||||||
else if (sin_ijk <= 0 && sin_ijk >= -MIN_SINE) sin_ijk = -MIN_SINE;
|
|
||||||
if (sin_jkl >= 0 && sin_jkl <= MIN_SINE) sin_jkl = MIN_SINE;
|
|
||||||
else if (sin_jkl <= 0 && sin_jkl >= -MIN_SINE) sin_jkl = -MIN_SINE;
|
|
||||||
|
|
||||||
// dcos_omega_di
|
// dcos_omega_di
|
||||||
rvec_ScaledSum(dcos_omega_di, (htra-arg*hnra)/r_ij, dvec_ij, -1., dvec_li);
|
rvec_ScaledSum(dcos_omega_di, (htra-arg*hnra)/r_ij, dvec_ij, -1., dvec_li);
|
||||||
rvec_ScaledAdd(dcos_omega_di,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_dk);
|
rvec_ScaledAdd(dcos_omega_di,-(hthd-arg*hnhd)/sin_ijk, p_ijk->dcos_dk);
|
||||||
|
|||||||
@ -253,9 +253,10 @@ void FixEHEX::rescale()
|
|||||||
|
|
||||||
escale = 1. + (F * dt) / Kr;
|
escale = 1. + (F * dt) / Kr;
|
||||||
|
|
||||||
// safety check for kinetic energy
|
// safety checks for kinetic energy rescaling
|
||||||
|
|
||||||
if (escale < 0.0) error->all(FLERR, "Fix ehex kinetic energy went negative");
|
if (escale < 0.0) error->all(FLERR, "Fix ehex kinetic energy went negative: {}", escale);
|
||||||
|
if (escale > 100.0) error->all(FLERR, "Fix ehex kinetic energy rescaling too large: {}", escale);
|
||||||
|
|
||||||
scale = sqrt(escale);
|
scale = sqrt(escale);
|
||||||
vsub[0] = (scale - 1.0) * vcm[0];
|
vsub[0] = (scale - 1.0) * vcm[0];
|
||||||
@ -569,7 +570,11 @@ void FixEHEX::com_properties(double *vr, double *sfr, double *sfvr, double *K, d
|
|||||||
|
|
||||||
*mr = buf[4];
|
*mr = buf[4];
|
||||||
|
|
||||||
if (*mr < 1.e-14) { error->all(FLERR, "Fix ehex error mass of region is close to zero"); }
|
if (nlocal > 0)
|
||||||
|
mi = (rmass) ? rmass[0] : mass[type[0]];
|
||||||
|
else
|
||||||
|
mi = 1.0;
|
||||||
|
if ((*mr / mi) < 1.e-14) error->all(FLERR, "Fix ehex error mass of region is close to zero");
|
||||||
|
|
||||||
// total kinetic energy of region
|
// total kinetic energy of region
|
||||||
|
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -19,8 +18,8 @@
|
|||||||
#include "angle_deprecated.h"
|
#include "angle_deprecated.h"
|
||||||
#include "angle_hybrid.h"
|
#include "angle_hybrid.h"
|
||||||
#include "comm.h"
|
#include "comm.h"
|
||||||
#include "force.h"
|
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
#include "force.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -33,17 +32,14 @@ void AngleDeprecated::settings(int, char **)
|
|||||||
// hybrid substyles are created in AngleHybrid::settings(), so when this is
|
// hybrid substyles are created in AngleHybrid::settings(), so when this is
|
||||||
// called, our style was just added at the end of the list of substyles
|
// called, our style was just added at the end of the list of substyles
|
||||||
|
|
||||||
if (utils::strmatch(my_style,"^hybrid")) {
|
if (utils::strmatch(my_style, "^hybrid")) {
|
||||||
auto hybrid = dynamic_cast<AngleHybrid *>(force->angle);
|
auto hybrid = dynamic_cast<AngleHybrid *>(force->angle);
|
||||||
my_style = hybrid->keywords[hybrid->nstyles];
|
my_style = hybrid->keywords[hybrid->nstyles];
|
||||||
}
|
}
|
||||||
|
|
||||||
if (my_style == "DEPRECATED") {
|
if (my_style == "DEPRECATED") {
|
||||||
if (lmp->comm->me == 0)
|
if (lmp->comm->me == 0) utils::logmesg(lmp, "\nAngle style 'DEPRECATED' is a dummy style\n\n");
|
||||||
utils::logmesg(lmp,"\nAngle style 'DEPRECATED' is a dummy style\n\n");
|
|
||||||
return;
|
return;
|
||||||
}
|
}
|
||||||
error->all(FLERR,"This angle style is no longer available");
|
error->all(FLERR, "This angle style is no longer available");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -29,5 +28,5 @@ Body::Body(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
|
|||||||
|
|
||||||
Body::~Body()
|
Body::~Body()
|
||||||
{
|
{
|
||||||
delete [] style;
|
delete[] style;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -34,17 +33,14 @@ void BondDeprecated::settings(int, char **)
|
|||||||
// hybrid substyles are created in BondHybrid::settings(), so when this is
|
// hybrid substyles are created in BondHybrid::settings(), so when this is
|
||||||
// called, our style was just added at the end of the list of substyles
|
// called, our style was just added at the end of the list of substyles
|
||||||
|
|
||||||
if (utils::strmatch(my_style,"^hybrid")) {
|
if (utils::strmatch(my_style, "^hybrid")) {
|
||||||
auto hybrid = dynamic_cast<BondHybrid *>(force->bond);
|
auto hybrid = dynamic_cast<BondHybrid *>(force->bond);
|
||||||
my_style = hybrid->keywords[hybrid->nstyles];
|
my_style = hybrid->keywords[hybrid->nstyles];
|
||||||
}
|
}
|
||||||
|
|
||||||
if (my_style == "DEPRECATED") {
|
if (my_style == "DEPRECATED") {
|
||||||
if (lmp->comm->me == 0)
|
if (lmp->comm->me == 0) utils::logmesg(lmp, "\nBond style 'DEPRECATED' is a dummy style\n\n");
|
||||||
utils::logmesg(lmp,"\nBond style 'DEPRECATED' is a dummy style\n\n");
|
|
||||||
return;
|
return;
|
||||||
}
|
}
|
||||||
error->all(FLERR,"This bond style is no longer available");
|
error->all(FLERR, "This bond style is no longer available");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -25,10 +24,9 @@ using namespace LAMMPS_NS;
|
|||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
ComputeAngle::ComputeAngle(LAMMPS *lmp, int narg, char **arg) :
|
ComputeAngle::ComputeAngle(LAMMPS *lmp, int narg, char **arg) :
|
||||||
Compute(lmp, narg, arg),
|
Compute(lmp, narg, arg), emine(nullptr)
|
||||||
emine(nullptr)
|
|
||||||
{
|
{
|
||||||
if (narg != 3) error->all(FLERR,"Illegal compute angle command");
|
if (narg != 3) error->all(FLERR, "Illegal compute angle command");
|
||||||
|
|
||||||
vector_flag = 1;
|
vector_flag = 1;
|
||||||
extvector = 1;
|
extvector = 1;
|
||||||
@ -37,9 +35,8 @@ ComputeAngle::ComputeAngle(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
// check if bond style hybrid exists
|
// check if bond style hybrid exists
|
||||||
|
|
||||||
angle = dynamic_cast<AngleHybrid *>( force->angle_match("hybrid"));
|
angle = dynamic_cast<AngleHybrid *>(force->angle_match("hybrid"));
|
||||||
if (!angle)
|
if (!angle) error->all(FLERR, "Angle style for compute angle command is not hybrid");
|
||||||
error->all(FLERR,"Angle style for compute angle command is not hybrid");
|
|
||||||
size_vector = nsub = angle->nstyles;
|
size_vector = nsub = angle->nstyles;
|
||||||
|
|
||||||
emine = new double[nsub];
|
emine = new double[nsub];
|
||||||
@ -50,8 +47,8 @@ ComputeAngle::ComputeAngle(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
ComputeAngle::~ComputeAngle()
|
ComputeAngle::~ComputeAngle()
|
||||||
{
|
{
|
||||||
delete [] emine;
|
delete[] emine;
|
||||||
delete [] vector;
|
delete[] vector;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -60,11 +57,10 @@ void ComputeAngle::init()
|
|||||||
{
|
{
|
||||||
// recheck angle style in case it has been changed
|
// recheck angle style in case it has been changed
|
||||||
|
|
||||||
angle = dynamic_cast<AngleHybrid *>( force->angle_match("hybrid"));
|
angle = dynamic_cast<AngleHybrid *>(force->angle_match("hybrid"));
|
||||||
if (!angle)
|
if (!angle) error->all(FLERR, "Angle style for compute angle command is not hybrid");
|
||||||
error->all(FLERR,"Angle style for compute angle command is not hybrid");
|
|
||||||
if (angle->nstyles != nsub)
|
if (angle->nstyles != nsub)
|
||||||
error->all(FLERR,"Angle style for compute angle command has changed");
|
error->all(FLERR, "Angle style for compute angle command has changed");
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -73,10 +69,9 @@ void ComputeAngle::compute_vector()
|
|||||||
{
|
{
|
||||||
invoked_vector = update->ntimestep;
|
invoked_vector = update->ntimestep;
|
||||||
if (update->eflag_global != invoked_vector)
|
if (update->eflag_global != invoked_vector)
|
||||||
error->all(FLERR,"Energy was not tallied on needed timestep");
|
error->all(FLERR, "Energy was not tallied on needed timestep");
|
||||||
|
|
||||||
for (int i = 0; i < nsub; i++)
|
for (int i = 0; i < nsub; i++) emine[i] = angle->styles[i]->energy;
|
||||||
emine[i] = angle->styles[i]->energy;
|
|
||||||
|
|
||||||
MPI_Allreduce(emine,vector,nsub,MPI_DOUBLE,MPI_SUM,world);
|
MPI_Allreduce(emine, vector, nsub, MPI_DOUBLE, MPI_SUM, world);
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -25,10 +24,9 @@ using namespace LAMMPS_NS;
|
|||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
ComputeBond::ComputeBond(LAMMPS *lmp, int narg, char **arg) :
|
ComputeBond::ComputeBond(LAMMPS *lmp, int narg, char **arg) :
|
||||||
Compute(lmp, narg, arg),
|
Compute(lmp, narg, arg), emine(nullptr)
|
||||||
emine(nullptr)
|
|
||||||
{
|
{
|
||||||
if (narg != 3) error->all(FLERR,"Illegal compute bond command");
|
if (narg != 3) error->all(FLERR, "Illegal compute bond command");
|
||||||
|
|
||||||
vector_flag = 1;
|
vector_flag = 1;
|
||||||
extvector = 1;
|
extvector = 1;
|
||||||
@ -37,9 +35,8 @@ ComputeBond::ComputeBond(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
// check if bond style hybrid exists
|
// check if bond style hybrid exists
|
||||||
|
|
||||||
bond = dynamic_cast<BondHybrid *>( force->bond_match("hybrid"));
|
bond = dynamic_cast<BondHybrid *>(force->bond_match("hybrid"));
|
||||||
if (!bond)
|
if (!bond) error->all(FLERR, "Bond style for compute bond command is not hybrid");
|
||||||
error->all(FLERR,"Bond style for compute bond command is not hybrid");
|
|
||||||
size_vector = nsub = bond->nstyles;
|
size_vector = nsub = bond->nstyles;
|
||||||
|
|
||||||
emine = new double[nsub];
|
emine = new double[nsub];
|
||||||
@ -50,8 +47,8 @@ ComputeBond::ComputeBond(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
ComputeBond::~ComputeBond()
|
ComputeBond::~ComputeBond()
|
||||||
{
|
{
|
||||||
delete [] emine;
|
delete[] emine;
|
||||||
delete [] vector;
|
delete[] vector;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -60,11 +57,9 @@ void ComputeBond::init()
|
|||||||
{
|
{
|
||||||
// recheck bond style in case it has been changed
|
// recheck bond style in case it has been changed
|
||||||
|
|
||||||
bond = dynamic_cast<BondHybrid *>( force->bond_match("hybrid"));
|
bond = dynamic_cast<BondHybrid *>(force->bond_match("hybrid"));
|
||||||
if (!bond)
|
if (!bond) error->all(FLERR, "Bond style for compute bond command is not hybrid");
|
||||||
error->all(FLERR,"Bond style for compute bond command is not hybrid");
|
if (bond->nstyles != nsub) error->all(FLERR, "Bond style for compute bond command has changed");
|
||||||
if (bond->nstyles != nsub)
|
|
||||||
error->all(FLERR,"Bond style for compute bond command has changed");
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -73,10 +68,9 @@ void ComputeBond::compute_vector()
|
|||||||
{
|
{
|
||||||
invoked_vector = update->ntimestep;
|
invoked_vector = update->ntimestep;
|
||||||
if (update->eflag_global != invoked_vector)
|
if (update->eflag_global != invoked_vector)
|
||||||
error->all(FLERR,"Energy was not tallied on needed timestep");
|
error->all(FLERR, "Energy was not tallied on needed timestep");
|
||||||
|
|
||||||
for (int i = 0; i < nsub; i++)
|
for (int i = 0; i < nsub; i++) emine[i] = bond->styles[i]->energy;
|
||||||
emine[i] = bond->styles[i]->energy;
|
|
||||||
|
|
||||||
MPI_Allreduce(emine,vector,nsub,MPI_DOUBLE,MPI_SUM,world);
|
MPI_Allreduce(emine, vector, nsub, MPI_DOUBLE, MPI_SUM, world);
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -13,18 +12,17 @@
|
|||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#include "compute_com.h"
|
#include "compute_com.h"
|
||||||
#include "update.h"
|
|
||||||
#include "group.h"
|
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
#include "group.h"
|
||||||
|
#include "update.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
ComputeCOM::ComputeCOM(LAMMPS *lmp, int narg, char **arg) :
|
ComputeCOM::ComputeCOM(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
|
||||||
Compute(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
if (narg != 3) error->all(FLERR,"Illegal compute com command");
|
if (narg != 3) error->all(FLERR, "Illegal compute com command");
|
||||||
|
|
||||||
vector_flag = 1;
|
vector_flag = 1;
|
||||||
size_vector = 3;
|
size_vector = 3;
|
||||||
@ -37,7 +35,7 @@ ComputeCOM::ComputeCOM(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
ComputeCOM::~ComputeCOM()
|
ComputeCOM::~ComputeCOM()
|
||||||
{
|
{
|
||||||
delete [] vector;
|
delete[] vector;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -54,5 +52,5 @@ void ComputeCOM::compute_vector()
|
|||||||
invoked_vector = update->ntimestep;
|
invoked_vector = update->ntimestep;
|
||||||
if (group->dynamic[igroup]) masstotal = group->mass(igroup);
|
if (group->dynamic[igroup]) masstotal = group->mass(igroup);
|
||||||
|
|
||||||
group->xcm(igroup,masstotal,vector);
|
group->xcm(igroup, masstotal, vector);
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -21,15 +20,14 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
ComputeDeprecated::ComputeDeprecated(LAMMPS *lmp, int narg, char **arg) :
|
ComputeDeprecated::ComputeDeprecated(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
|
||||||
Compute(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
std::string my_style = style;
|
std::string my_style = style;
|
||||||
|
|
||||||
if (my_style == "DEPRECATED") {
|
if (my_style == "DEPRECATED") {
|
||||||
if (lmp->comm->me == 0)
|
if (lmp->comm->me == 0)
|
||||||
utils::logmesg(lmp,"\nCompute style 'DEPRECATED' is a dummy style\n\n");
|
utils::logmesg(lmp, "\nCompute style 'DEPRECATED' is a dummy style\n\n");
|
||||||
return;
|
return;
|
||||||
}
|
}
|
||||||
error->all(FLERR,"This compute style is no longer available");
|
error->all(FLERR, "This compute style is no longer available");
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -25,10 +24,9 @@ using namespace LAMMPS_NS;
|
|||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
ComputeDihedral::ComputeDihedral(LAMMPS *lmp, int narg, char **arg) :
|
ComputeDihedral::ComputeDihedral(LAMMPS *lmp, int narg, char **arg) :
|
||||||
Compute(lmp, narg, arg),
|
Compute(lmp, narg, arg), emine(nullptr)
|
||||||
emine(nullptr)
|
|
||||||
{
|
{
|
||||||
if (narg != 3) error->all(FLERR,"Illegal compute dihedral command");
|
if (narg != 3) error->all(FLERR, "Illegal compute dihedral command");
|
||||||
|
|
||||||
vector_flag = 1;
|
vector_flag = 1;
|
||||||
extvector = 1;
|
extvector = 1;
|
||||||
@ -37,9 +35,8 @@ ComputeDihedral::ComputeDihedral(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
// check if dihedral style hybrid exists
|
// check if dihedral style hybrid exists
|
||||||
|
|
||||||
dihedral = dynamic_cast<DihedralHybrid *>( force->dihedral_match("hybrid"));
|
dihedral = dynamic_cast<DihedralHybrid *>(force->dihedral_match("hybrid"));
|
||||||
if (!dihedral)
|
if (!dihedral) error->all(FLERR, "Dihedral style for compute dihedral command is not hybrid");
|
||||||
error->all(FLERR, "Dihedral style for compute dihedral command is not hybrid");
|
|
||||||
size_vector = nsub = dihedral->nstyles;
|
size_vector = nsub = dihedral->nstyles;
|
||||||
|
|
||||||
emine = new double[nsub];
|
emine = new double[nsub];
|
||||||
@ -50,8 +47,8 @@ ComputeDihedral::ComputeDihedral(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
ComputeDihedral::~ComputeDihedral()
|
ComputeDihedral::~ComputeDihedral()
|
||||||
{
|
{
|
||||||
delete [] emine;
|
delete[] emine;
|
||||||
delete [] vector;
|
delete[] vector;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -60,11 +57,10 @@ void ComputeDihedral::init()
|
|||||||
{
|
{
|
||||||
// recheck dihedral style in case it has been changed
|
// recheck dihedral style in case it has been changed
|
||||||
|
|
||||||
dihedral = dynamic_cast<DihedralHybrid *>( force->dihedral_match("hybrid"));
|
dihedral = dynamic_cast<DihedralHybrid *>(force->dihedral_match("hybrid"));
|
||||||
if (!dihedral)
|
if (!dihedral) error->all(FLERR, "Dihedral style for compute dihedral command is not hybrid");
|
||||||
error->all(FLERR, "Dihedral style for compute dihedral command is not hybrid");
|
|
||||||
if (dihedral->nstyles != nsub)
|
if (dihedral->nstyles != nsub)
|
||||||
error->all(FLERR,"Dihedral style for compute dihedral command has changed");
|
error->all(FLERR, "Dihedral style for compute dihedral command has changed");
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -73,10 +69,9 @@ void ComputeDihedral::compute_vector()
|
|||||||
{
|
{
|
||||||
invoked_vector = update->ntimestep;
|
invoked_vector = update->ntimestep;
|
||||||
if (update->eflag_global != invoked_vector)
|
if (update->eflag_global != invoked_vector)
|
||||||
error->all(FLERR,"Energy was not tallied on needed timestep");
|
error->all(FLERR, "Energy was not tallied on needed timestep");
|
||||||
|
|
||||||
for (int i = 0; i < nsub; i++)
|
for (int i = 0; i < nsub; i++) emine[i] = dihedral->styles[i]->energy;
|
||||||
emine[i] = dihedral->styles[i]->energy;
|
|
||||||
|
|
||||||
MPI_Allreduce(emine,vector,nsub,MPI_DOUBLE,MPI_SUM,world);
|
MPI_Allreduce(emine, vector, nsub, MPI_DOUBLE, MPI_SUM, world);
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -21,22 +20,21 @@
|
|||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
#define INERTIA 0.4 // moment of inertia prefactor for sphere
|
#define INERTIA 0.4 // moment of inertia prefactor for sphere
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
ComputeERotateSphere::ComputeERotateSphere(LAMMPS *lmp, int narg, char **arg) :
|
ComputeERotateSphere::ComputeERotateSphere(LAMMPS *lmp, int narg, char **arg) :
|
||||||
Compute(lmp, narg, arg)
|
Compute(lmp, narg, arg)
|
||||||
{
|
{
|
||||||
if (narg != 3) error->all(FLERR,"Illegal compute erotate/sphere command");
|
if (narg != 3) error->all(FLERR, "Illegal compute erotate/sphere command");
|
||||||
|
|
||||||
scalar_flag = 1;
|
scalar_flag = 1;
|
||||||
extscalar = 1;
|
extscalar = 1;
|
||||||
|
|
||||||
// error check
|
// error check
|
||||||
|
|
||||||
if (!atom->sphere_flag)
|
if (!atom->sphere_flag) error->all(FLERR, "Compute erotate/sphere requires atom style sphere");
|
||||||
error->all(FLERR,"Compute erotate/sphere requires atom style sphere");
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -64,10 +62,11 @@ double ComputeERotateSphere::compute_scalar()
|
|||||||
double erotate = 0.0;
|
double erotate = 0.0;
|
||||||
for (int i = 0; i < nlocal; i++)
|
for (int i = 0; i < nlocal; i++)
|
||||||
if (mask[i] & groupbit)
|
if (mask[i] & groupbit)
|
||||||
erotate += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
|
erotate +=
|
||||||
omega[i][2]*omega[i][2]) * radius[i]*radius[i]*rmass[i];
|
(omega[i][0] * omega[i][0] + omega[i][1] * omega[i][1] + omega[i][2] * omega[i][2]) *
|
||||||
|
radius[i] * radius[i] * rmass[i];
|
||||||
|
|
||||||
MPI_Allreduce(&erotate,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
|
MPI_Allreduce(&erotate, &scalar, 1, MPI_DOUBLE, MPI_SUM, world);
|
||||||
scalar *= pfactor;
|
scalar *= pfactor;
|
||||||
return scalar;
|
return scalar;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -14,21 +13,20 @@
|
|||||||
|
|
||||||
#include "compute_improper.h"
|
#include "compute_improper.h"
|
||||||
|
|
||||||
#include "update.h"
|
#include "error.h"
|
||||||
#include "force.h"
|
#include "force.h"
|
||||||
#include "improper.h"
|
#include "improper.h"
|
||||||
#include "improper_hybrid.h"
|
#include "improper_hybrid.h"
|
||||||
#include "error.h"
|
#include "update.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
ComputeImproper::ComputeImproper(LAMMPS *lmp, int narg, char **arg) :
|
ComputeImproper::ComputeImproper(LAMMPS *lmp, int narg, char **arg) :
|
||||||
Compute(lmp, narg, arg),
|
Compute(lmp, narg, arg), emine(nullptr)
|
||||||
emine(nullptr)
|
|
||||||
{
|
{
|
||||||
if (narg != 3) error->all(FLERR,"Illegal compute improper command");
|
if (narg != 3) error->all(FLERR, "Illegal compute improper command");
|
||||||
|
|
||||||
vector_flag = 1;
|
vector_flag = 1;
|
||||||
extvector = 1;
|
extvector = 1;
|
||||||
@ -37,9 +35,8 @@ ComputeImproper::ComputeImproper(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
// check if improper style hybrid exists
|
// check if improper style hybrid exists
|
||||||
|
|
||||||
improper = dynamic_cast<ImproperHybrid *>( force->improper_match("hybrid"));
|
improper = dynamic_cast<ImproperHybrid *>(force->improper_match("hybrid"));
|
||||||
if (!improper)
|
if (!improper) error->all(FLERR, "Improper style for compute improper command is not hybrid");
|
||||||
error->all(FLERR, "Improper style for compute improper command is not hybrid");
|
|
||||||
size_vector = nsub = improper->nstyles;
|
size_vector = nsub = improper->nstyles;
|
||||||
|
|
||||||
emine = new double[nsub];
|
emine = new double[nsub];
|
||||||
@ -50,8 +47,8 @@ ComputeImproper::ComputeImproper(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
ComputeImproper::~ComputeImproper()
|
ComputeImproper::~ComputeImproper()
|
||||||
{
|
{
|
||||||
delete [] emine;
|
delete[] emine;
|
||||||
delete [] vector;
|
delete[] vector;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -60,11 +57,10 @@ void ComputeImproper::init()
|
|||||||
{
|
{
|
||||||
// recheck improper style in case it has been changed
|
// recheck improper style in case it has been changed
|
||||||
|
|
||||||
improper = dynamic_cast<ImproperHybrid *>( force->improper_match("hybrid"));
|
improper = dynamic_cast<ImproperHybrid *>(force->improper_match("hybrid"));
|
||||||
if (!improper)
|
if (!improper) error->all(FLERR, "Improper style for compute improper command is not hybrid");
|
||||||
error->all(FLERR, "Improper style for compute improper command is not hybrid");
|
|
||||||
if (improper->nstyles != nsub)
|
if (improper->nstyles != nsub)
|
||||||
error->all(FLERR,"Improper style for compute improper command has changed");
|
error->all(FLERR, "Improper style for compute improper command has changed");
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -73,10 +69,9 @@ void ComputeImproper::compute_vector()
|
|||||||
{
|
{
|
||||||
invoked_vector = update->ntimestep;
|
invoked_vector = update->ntimestep;
|
||||||
if (update->eflag_global != invoked_vector)
|
if (update->eflag_global != invoked_vector)
|
||||||
error->all(FLERR,"Energy was not tallied on needed timestep");
|
error->all(FLERR, "Energy was not tallied on needed timestep");
|
||||||
|
|
||||||
for (int i = 0; i < nsub; i++)
|
for (int i = 0; i < nsub; i++) emine[i] = improper->styles[i]->energy;
|
||||||
emine[i] = improper->styles[i]->energy;
|
|
||||||
|
|
||||||
MPI_Allreduce(emine,vector,nsub,MPI_DOUBLE,MPI_SUM,world);
|
MPI_Allreduce(emine, vector, nsub, MPI_DOUBLE, MPI_SUM, world);
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -15,18 +14,17 @@
|
|||||||
#include "compute_ke.h"
|
#include "compute_ke.h"
|
||||||
|
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "update.h"
|
|
||||||
#include "force.h"
|
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "update.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
ComputeKE::ComputeKE(LAMMPS *lmp, int narg, char **arg) :
|
ComputeKE::ComputeKE(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
|
||||||
Compute(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
if (narg != 3) error->all(FLERR,"Illegal compute ke command");
|
if (narg != 3) error->all(FLERR, "Illegal compute ke command");
|
||||||
|
|
||||||
scalar_flag = 1;
|
scalar_flag = 1;
|
||||||
extscalar = 1;
|
extscalar = 1;
|
||||||
@ -57,15 +55,14 @@ double ComputeKE::compute_scalar()
|
|||||||
if (rmass) {
|
if (rmass) {
|
||||||
for (int i = 0; i < nlocal; i++)
|
for (int i = 0; i < nlocal; i++)
|
||||||
if (mask[i] & groupbit)
|
if (mask[i] & groupbit)
|
||||||
ke += rmass[i] * (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
|
ke += rmass[i] * (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]);
|
||||||
} else {
|
} else {
|
||||||
for (int i = 0; i < nlocal; i++)
|
for (int i = 0; i < nlocal; i++)
|
||||||
if (mask[i] & groupbit)
|
if (mask[i] & groupbit)
|
||||||
ke += mass[type[i]] *
|
ke += mass[type[i]] * (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]);
|
||||||
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
MPI_Allreduce(&ke,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
|
MPI_Allreduce(&ke, &scalar, 1, MPI_DOUBLE, MPI_SUM, world);
|
||||||
scalar *= pfactor;
|
scalar *= pfactor;
|
||||||
return scalar;
|
return scalar;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -33,15 +32,14 @@
|
|||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
enum{NOBIAS,BIAS};
|
enum { NOBIAS, BIAS };
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
|
ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||||
Compute(lmp, narg, arg),
|
Compute(lmp, narg, arg), id_temp(nullptr), stress(nullptr)
|
||||||
id_temp(nullptr), stress(nullptr)
|
|
||||||
{
|
{
|
||||||
if (narg < 4) error->all(FLERR,"Illegal compute stress/atom command");
|
if (narg < 4) error->all(FLERR, "Illegal compute stress/atom command");
|
||||||
|
|
||||||
peratom_flag = 1;
|
peratom_flag = 1;
|
||||||
size_peratom_cols = 6;
|
size_peratom_cols = 6;
|
||||||
@ -52,17 +50,15 @@ ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
// store temperature ID used by stress computation
|
// store temperature ID used by stress computation
|
||||||
// insure it is valid for temperature computation
|
// insure it is valid for temperature computation
|
||||||
|
|
||||||
if (strcmp(arg[3],"NULL") == 0) id_temp = nullptr;
|
if (strcmp(arg[3], "NULL") == 0)
|
||||||
|
id_temp = nullptr;
|
||||||
else {
|
else {
|
||||||
id_temp = utils::strdup(arg[3]);
|
id_temp = utils::strdup(arg[3]);
|
||||||
|
|
||||||
int icompute = modify->find_compute(id_temp);
|
int icompute = modify->find_compute(id_temp);
|
||||||
if (icompute < 0)
|
if (icompute < 0) error->all(FLERR, "Could not find compute stress/atom temperature ID");
|
||||||
error->all(FLERR,"Could not find compute stress/atom temperature ID");
|
|
||||||
if (modify->compute[icompute]->tempflag == 0)
|
if (modify->compute[icompute]->tempflag == 0)
|
||||||
error->all(FLERR,
|
error->all(FLERR, "Compute stress/atom temperature ID does not compute temperature");
|
||||||
"Compute stress/atom temperature ID does not "
|
|
||||||
"compute temperature");
|
|
||||||
}
|
}
|
||||||
|
|
||||||
// process optional args
|
// process optional args
|
||||||
@ -81,19 +77,28 @@ ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
fixflag = 0;
|
fixflag = 0;
|
||||||
int iarg = 4;
|
int iarg = 4;
|
||||||
while (iarg < narg) {
|
while (iarg < narg) {
|
||||||
if (strcmp(arg[iarg],"ke") == 0) keflag = 1;
|
if (strcmp(arg[iarg], "ke") == 0)
|
||||||
else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
|
keflag = 1;
|
||||||
else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
|
else if (strcmp(arg[iarg], "pair") == 0)
|
||||||
else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
|
pairflag = 1;
|
||||||
else if (strcmp(arg[iarg],"dihedral") == 0) dihedralflag = 1;
|
else if (strcmp(arg[iarg], "bond") == 0)
|
||||||
else if (strcmp(arg[iarg],"improper") == 0) improperflag = 1;
|
bondflag = 1;
|
||||||
else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
|
else if (strcmp(arg[iarg], "angle") == 0)
|
||||||
else if (strcmp(arg[iarg],"fix") == 0) fixflag = 1;
|
angleflag = 1;
|
||||||
else if (strcmp(arg[iarg],"virial") == 0) {
|
else if (strcmp(arg[iarg], "dihedral") == 0)
|
||||||
|
dihedralflag = 1;
|
||||||
|
else if (strcmp(arg[iarg], "improper") == 0)
|
||||||
|
improperflag = 1;
|
||||||
|
else if (strcmp(arg[iarg], "kspace") == 0)
|
||||||
|
kspaceflag = 1;
|
||||||
|
else if (strcmp(arg[iarg], "fix") == 0)
|
||||||
|
fixflag = 1;
|
||||||
|
else if (strcmp(arg[iarg], "virial") == 0) {
|
||||||
pairflag = 1;
|
pairflag = 1;
|
||||||
bondflag = angleflag = dihedralflag = improperflag = 1;
|
bondflag = angleflag = dihedralflag = improperflag = 1;
|
||||||
kspaceflag = fixflag = 1;
|
kspaceflag = fixflag = 1;
|
||||||
} else error->all(FLERR,"Illegal compute stress/atom command");
|
} else
|
||||||
|
error->all(FLERR, "Illegal compute stress/atom command");
|
||||||
iarg++;
|
iarg++;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -105,7 +110,7 @@ ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
ComputeStressAtom::~ComputeStressAtom()
|
ComputeStressAtom::~ComputeStressAtom()
|
||||||
{
|
{
|
||||||
delete [] id_temp;
|
delete[] id_temp;
|
||||||
memory->destroy(stress);
|
memory->destroy(stress);
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -118,24 +123,26 @@ void ComputeStressAtom::init()
|
|||||||
|
|
||||||
if (id_temp) {
|
if (id_temp) {
|
||||||
int icompute = modify->find_compute(id_temp);
|
int icompute = modify->find_compute(id_temp);
|
||||||
if (icompute < 0)
|
if (icompute < 0) error->all(FLERR, "Could not find compute stress/atom temperature ID");
|
||||||
error->all(FLERR,"Could not find compute stress/atom temperature ID");
|
|
||||||
temperature = modify->compute[icompute];
|
temperature = modify->compute[icompute];
|
||||||
if (temperature->tempbias) biasflag = BIAS;
|
if (temperature->tempbias)
|
||||||
else biasflag = NOBIAS;
|
biasflag = BIAS;
|
||||||
} else biasflag = NOBIAS;
|
else
|
||||||
|
biasflag = NOBIAS;
|
||||||
|
} else
|
||||||
|
biasflag = NOBIAS;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void ComputeStressAtom::compute_peratom()
|
void ComputeStressAtom::compute_peratom()
|
||||||
{
|
{
|
||||||
int i,j;
|
int i, j;
|
||||||
double onemass;
|
double onemass;
|
||||||
|
|
||||||
invoked_peratom = update->ntimestep;
|
invoked_peratom = update->ntimestep;
|
||||||
if (update->vflag_atom != invoked_peratom)
|
if (update->vflag_atom != invoked_peratom)
|
||||||
error->all(FLERR,"Per-atom virial was not tallied on needed timestep");
|
error->all(FLERR, "Per-atom virial was not tallied on needed timestep");
|
||||||
|
|
||||||
// grow local stress array if necessary
|
// grow local stress array if necessary
|
||||||
// needs to be atom->nmax in length
|
// needs to be atom->nmax in length
|
||||||
@ -143,7 +150,7 @@ void ComputeStressAtom::compute_peratom()
|
|||||||
if (atom->nmax > nmax) {
|
if (atom->nmax > nmax) {
|
||||||
memory->destroy(stress);
|
memory->destroy(stress);
|
||||||
nmax = atom->nmax;
|
nmax = atom->nmax;
|
||||||
memory->create(stress,nmax,6,"stress/atom:stress");
|
memory->create(stress, nmax, 6, "stress/atom:stress");
|
||||||
array_atom = stress;
|
array_atom = stress;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -166,51 +173,44 @@ void ComputeStressAtom::compute_peratom()
|
|||||||
// clear local stress array
|
// clear local stress array
|
||||||
|
|
||||||
for (i = 0; i < ntotal; i++)
|
for (i = 0; i < ntotal; i++)
|
||||||
for (j = 0; j < 6; j++)
|
for (j = 0; j < 6; j++) stress[i][j] = 0.0;
|
||||||
stress[i][j] = 0.0;
|
|
||||||
|
|
||||||
// add in per-atom contributions from each force
|
// add in per-atom contributions from each force
|
||||||
|
|
||||||
if (pairflag && force->pair && force->pair->compute_flag) {
|
if (pairflag && force->pair && force->pair->compute_flag) {
|
||||||
double **vatom = force->pair->vatom;
|
double **vatom = force->pair->vatom;
|
||||||
for (i = 0; i < npair; i++)
|
for (i = 0; i < npair; i++)
|
||||||
for (j = 0; j < 6; j++)
|
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
|
||||||
stress[i][j] += vatom[i][j];
|
|
||||||
}
|
}
|
||||||
|
|
||||||
if (bondflag && force->bond) {
|
if (bondflag && force->bond) {
|
||||||
double **vatom = force->bond->vatom;
|
double **vatom = force->bond->vatom;
|
||||||
for (i = 0; i < nbond; i++)
|
for (i = 0; i < nbond; i++)
|
||||||
for (j = 0; j < 6; j++)
|
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
|
||||||
stress[i][j] += vatom[i][j];
|
|
||||||
}
|
}
|
||||||
|
|
||||||
if (angleflag && force->angle) {
|
if (angleflag && force->angle) {
|
||||||
double **vatom = force->angle->vatom;
|
double **vatom = force->angle->vatom;
|
||||||
for (i = 0; i < nbond; i++)
|
for (i = 0; i < nbond; i++)
|
||||||
for (j = 0; j < 6; j++)
|
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
|
||||||
stress[i][j] += vatom[i][j];
|
|
||||||
}
|
}
|
||||||
|
|
||||||
if (dihedralflag && force->dihedral) {
|
if (dihedralflag && force->dihedral) {
|
||||||
double **vatom = force->dihedral->vatom;
|
double **vatom = force->dihedral->vatom;
|
||||||
for (i = 0; i < nbond; i++)
|
for (i = 0; i < nbond; i++)
|
||||||
for (j = 0; j < 6; j++)
|
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
|
||||||
stress[i][j] += vatom[i][j];
|
|
||||||
}
|
}
|
||||||
|
|
||||||
if (improperflag && force->improper) {
|
if (improperflag && force->improper) {
|
||||||
double **vatom = force->improper->vatom;
|
double **vatom = force->improper->vatom;
|
||||||
for (i = 0; i < nbond; i++)
|
for (i = 0; i < nbond; i++)
|
||||||
for (j = 0; j < 6; j++)
|
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
|
||||||
stress[i][j] += vatom[i][j];
|
|
||||||
}
|
}
|
||||||
|
|
||||||
if (kspaceflag && force->kspace && force->kspace->compute_flag) {
|
if (kspaceflag && force->kspace && force->kspace->compute_flag) {
|
||||||
double **vatom = force->kspace->vatom;
|
double **vatom = force->kspace->vatom;
|
||||||
for (i = 0; i < nkspace; i++)
|
for (i = 0; i < nkspace; i++)
|
||||||
for (j = 0; j < 6; j++)
|
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
|
||||||
stress[i][j] += vatom[i][j];
|
|
||||||
}
|
}
|
||||||
|
|
||||||
// add in per-atom contributions from relevant fixes
|
// add in per-atom contributions from relevant fixes
|
||||||
@ -225,15 +225,13 @@ void ComputeStressAtom::compute_peratom()
|
|||||||
double **vatom = ifix->vatom;
|
double **vatom = ifix->vatom;
|
||||||
if (vatom)
|
if (vatom)
|
||||||
for (i = 0; i < nlocal; i++)
|
for (i = 0; i < nlocal; i++)
|
||||||
for (j = 0; j < 6; j++)
|
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
|
||||||
stress[i][j] += vatom[i][j];
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
// communicate ghost virials between neighbor procs
|
// communicate ghost virials between neighbor procs
|
||||||
|
|
||||||
if (force->newton || (force->kspace && force->kspace->tip4pflag))
|
if (force->newton || (force->kspace && force->kspace->tip4pflag)) comm->reverse_comm(this);
|
||||||
comm->reverse_comm(this);
|
|
||||||
|
|
||||||
// zero virial of atoms not in group
|
// zero virial of atoms not in group
|
||||||
// only do this after comm since ghost contributions must be included
|
// only do this after comm since ghost contributions must be included
|
||||||
@ -266,24 +264,24 @@ void ComputeStressAtom::compute_peratom()
|
|||||||
for (i = 0; i < nlocal; i++)
|
for (i = 0; i < nlocal; i++)
|
||||||
if (mask[i] & groupbit) {
|
if (mask[i] & groupbit) {
|
||||||
onemass = mvv2e * rmass[i];
|
onemass = mvv2e * rmass[i];
|
||||||
stress[i][0] += onemass*v[i][0]*v[i][0];
|
stress[i][0] += onemass * v[i][0] * v[i][0];
|
||||||
stress[i][1] += onemass*v[i][1]*v[i][1];
|
stress[i][1] += onemass * v[i][1] * v[i][1];
|
||||||
stress[i][2] += onemass*v[i][2]*v[i][2];
|
stress[i][2] += onemass * v[i][2] * v[i][2];
|
||||||
stress[i][3] += onemass*v[i][0]*v[i][1];
|
stress[i][3] += onemass * v[i][0] * v[i][1];
|
||||||
stress[i][4] += onemass*v[i][0]*v[i][2];
|
stress[i][4] += onemass * v[i][0] * v[i][2];
|
||||||
stress[i][5] += onemass*v[i][1]*v[i][2];
|
stress[i][5] += onemass * v[i][1] * v[i][2];
|
||||||
}
|
}
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
for (i = 0; i < nlocal; i++)
|
for (i = 0; i < nlocal; i++)
|
||||||
if (mask[i] & groupbit) {
|
if (mask[i] & groupbit) {
|
||||||
onemass = mvv2e * mass[type[i]];
|
onemass = mvv2e * mass[type[i]];
|
||||||
stress[i][0] += onemass*v[i][0]*v[i][0];
|
stress[i][0] += onemass * v[i][0] * v[i][0];
|
||||||
stress[i][1] += onemass*v[i][1]*v[i][1];
|
stress[i][1] += onemass * v[i][1] * v[i][1];
|
||||||
stress[i][2] += onemass*v[i][2]*v[i][2];
|
stress[i][2] += onemass * v[i][2] * v[i][2];
|
||||||
stress[i][3] += onemass*v[i][0]*v[i][1];
|
stress[i][3] += onemass * v[i][0] * v[i][1];
|
||||||
stress[i][4] += onemass*v[i][0]*v[i][2];
|
stress[i][4] += onemass * v[i][0] * v[i][2];
|
||||||
stress[i][5] += onemass*v[i][1]*v[i][2];
|
stress[i][5] += onemass * v[i][1] * v[i][2];
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -292,35 +290,34 @@ void ComputeStressAtom::compute_peratom()
|
|||||||
// invoke temperature if it hasn't been already
|
// invoke temperature if it hasn't been already
|
||||||
// this insures bias factor is pre-computed
|
// this insures bias factor is pre-computed
|
||||||
|
|
||||||
if (keflag && temperature->invoked_scalar != update->ntimestep)
|
if (keflag && temperature->invoked_scalar != update->ntimestep) temperature->compute_scalar();
|
||||||
temperature->compute_scalar();
|
|
||||||
|
|
||||||
if (rmass) {
|
if (rmass) {
|
||||||
for (i = 0; i < nlocal; i++)
|
for (i = 0; i < nlocal; i++)
|
||||||
if (mask[i] & groupbit) {
|
if (mask[i] & groupbit) {
|
||||||
temperature->remove_bias(i,v[i]);
|
temperature->remove_bias(i, v[i]);
|
||||||
onemass = mvv2e * rmass[i];
|
onemass = mvv2e * rmass[i];
|
||||||
stress[i][0] += onemass*v[i][0]*v[i][0];
|
stress[i][0] += onemass * v[i][0] * v[i][0];
|
||||||
stress[i][1] += onemass*v[i][1]*v[i][1];
|
stress[i][1] += onemass * v[i][1] * v[i][1];
|
||||||
stress[i][2] += onemass*v[i][2]*v[i][2];
|
stress[i][2] += onemass * v[i][2] * v[i][2];
|
||||||
stress[i][3] += onemass*v[i][0]*v[i][1];
|
stress[i][3] += onemass * v[i][0] * v[i][1];
|
||||||
stress[i][4] += onemass*v[i][0]*v[i][2];
|
stress[i][4] += onemass * v[i][0] * v[i][2];
|
||||||
stress[i][5] += onemass*v[i][1]*v[i][2];
|
stress[i][5] += onemass * v[i][1] * v[i][2];
|
||||||
temperature->restore_bias(i,v[i]);
|
temperature->restore_bias(i, v[i]);
|
||||||
}
|
}
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
for (i = 0; i < nlocal; i++)
|
for (i = 0; i < nlocal; i++)
|
||||||
if (mask[i] & groupbit) {
|
if (mask[i] & groupbit) {
|
||||||
temperature->remove_bias(i,v[i]);
|
temperature->remove_bias(i, v[i]);
|
||||||
onemass = mvv2e * mass[type[i]];
|
onemass = mvv2e * mass[type[i]];
|
||||||
stress[i][0] += onemass*v[i][0]*v[i][0];
|
stress[i][0] += onemass * v[i][0] * v[i][0];
|
||||||
stress[i][1] += onemass*v[i][1]*v[i][1];
|
stress[i][1] += onemass * v[i][1] * v[i][1];
|
||||||
stress[i][2] += onemass*v[i][2]*v[i][2];
|
stress[i][2] += onemass * v[i][2] * v[i][2];
|
||||||
stress[i][3] += onemass*v[i][0]*v[i][1];
|
stress[i][3] += onemass * v[i][0] * v[i][1];
|
||||||
stress[i][4] += onemass*v[i][0]*v[i][2];
|
stress[i][4] += onemass * v[i][0] * v[i][2];
|
||||||
stress[i][5] += onemass*v[i][1]*v[i][2];
|
stress[i][5] += onemass * v[i][1] * v[i][2];
|
||||||
temperature->restore_bias(i,v[i]);
|
temperature->restore_bias(i, v[i]);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -344,7 +341,7 @@ void ComputeStressAtom::compute_peratom()
|
|||||||
|
|
||||||
int ComputeStressAtom::pack_reverse_comm(int n, int first, double *buf)
|
int ComputeStressAtom::pack_reverse_comm(int n, int first, double *buf)
|
||||||
{
|
{
|
||||||
int i,m,last;
|
int i, m, last;
|
||||||
|
|
||||||
m = 0;
|
m = 0;
|
||||||
last = first + n;
|
last = first + n;
|
||||||
@ -363,7 +360,7 @@ int ComputeStressAtom::pack_reverse_comm(int n, int first, double *buf)
|
|||||||
|
|
||||||
void ComputeStressAtom::unpack_reverse_comm(int n, int *list, double *buf)
|
void ComputeStressAtom::unpack_reverse_comm(int n, int *list, double *buf)
|
||||||
{
|
{
|
||||||
int i,j,m;
|
int i, j, m;
|
||||||
|
|
||||||
m = 0;
|
m = 0;
|
||||||
for (i = 0; i < n; i++) {
|
for (i = 0; i < n; i++) {
|
||||||
@ -383,6 +380,6 @@ void ComputeStressAtom::unpack_reverse_comm(int n, int *list, double *buf)
|
|||||||
|
|
||||||
double ComputeStressAtom::memory_usage()
|
double ComputeStressAtom::memory_usage()
|
||||||
{
|
{
|
||||||
double bytes = (double)nmax*6 * sizeof(double);
|
double bytes = (double) nmax * 6 * sizeof(double);
|
||||||
return bytes;
|
return bytes;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -23,7 +22,6 @@
|
|||||||
#include "error.h"
|
#include "error.h"
|
||||||
#include "force.h"
|
#include "force.h"
|
||||||
|
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -36,15 +34,15 @@ void DihedralDeprecated::settings(int, char **)
|
|||||||
// so when this is called, our style was just added at the end
|
// so when this is called, our style was just added at the end
|
||||||
// of the list of substyles
|
// of the list of substyles
|
||||||
|
|
||||||
if (utils::strmatch(my_style,"^hybrid")) {
|
if (utils::strmatch(my_style, "^hybrid")) {
|
||||||
auto hybrid = dynamic_cast<DihedralHybrid *>(force->dihedral);
|
auto hybrid = dynamic_cast<DihedralHybrid *>(force->dihedral);
|
||||||
my_style = hybrid->keywords[hybrid->nstyles];
|
my_style = hybrid->keywords[hybrid->nstyles];
|
||||||
}
|
}
|
||||||
|
|
||||||
if (my_style == "DEPRECATED") {
|
if (my_style == "DEPRECATED") {
|
||||||
if (lmp->comm->me == 0)
|
if (lmp->comm->me == 0)
|
||||||
utils::logmesg(lmp,"\nDihedral style 'DEPRECATED' is a dummy style\n\n");
|
utils::logmesg(lmp, "\nDihedral style 'DEPRECATED' is a dummy style\n\n");
|
||||||
return;
|
return;
|
||||||
}
|
}
|
||||||
error->all(FLERR,"This dihedral style is no longer available");
|
error->all(FLERR, "This dihedral style is no longer available");
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -21,15 +20,13 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
DumpDeprecated::DumpDeprecated(LAMMPS *lmp, int narg, char **arg) :
|
DumpDeprecated::DumpDeprecated(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
|
||||||
Dump(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
std::string my_style = style;
|
std::string my_style = style;
|
||||||
|
|
||||||
if (my_style == "DEPRECATED") {
|
if (my_style == "DEPRECATED") {
|
||||||
if (lmp->comm->me == 0)
|
if (lmp->comm->me == 0) utils::logmesg(lmp, "\nDump style 'DEPRECATED' is a dummy style\n\n");
|
||||||
utils::logmesg(lmp,"\nDump style 'DEPRECATED' is a dummy style\n\n");
|
|
||||||
return;
|
return;
|
||||||
}
|
}
|
||||||
error->all(FLERR,"This dump style is no longer available");
|
error->all(FLERR, "This dump style is no longer available");
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -17,23 +16,21 @@
|
|||||||
#include "comm.h"
|
#include "comm.h"
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
FixDeprecated::FixDeprecated(LAMMPS *lmp, int narg, char **arg) :
|
FixDeprecated::FixDeprecated(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||||
Fix(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
std::string my_style = style;
|
std::string my_style = style;
|
||||||
|
|
||||||
if (my_style == "DEPRECATED") {
|
if (my_style == "DEPRECATED") {
|
||||||
if (lmp->comm->me == 0)
|
if (lmp->comm->me == 0) utils::logmesg(lmp, "\nFix style 'DEPRECATED' is a dummy style\n\n");
|
||||||
utils::logmesg(lmp,"\nFix style 'DEPRECATED' is a dummy style\n\n");
|
|
||||||
return;
|
return;
|
||||||
} else if (utils::strmatch(my_style,"^ave/spatial")) {
|
} else if (utils::strmatch(my_style, "^ave/spatial")) {
|
||||||
if (lmp->comm->me == 0)
|
if (lmp->comm->me == 0)
|
||||||
utils::logmesg(lmp,"\nFix styles 'ave/spatial' and 'ave/spatial/sphere'"
|
utils::logmesg(lmp,
|
||||||
|
"\nFix styles 'ave/spatial' and 'ave/spatial/sphere'"
|
||||||
" have been replaced\nby the more general fix ave/chunk "
|
" have been replaced\nby the more general fix ave/chunk "
|
||||||
"and compute chunk/atom commands.\nAll ave/spatial and "
|
"and compute chunk/atom commands.\nAll ave/spatial and "
|
||||||
"ave/spatial/sphere functionality is available in these"
|
"ave/spatial/sphere functionality is available in these"
|
||||||
@ -44,14 +41,16 @@ FixDeprecated::FixDeprecated(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
"compute chunk/atom:\n dim, origin, delta, region, "
|
"compute chunk/atom:\n dim, origin, delta, region, "
|
||||||
"bound, discard, units\n\n");
|
"bound, discard, units\n\n");
|
||||||
} else if (my_style == "lb/pc") {
|
} else if (my_style == "lb/pc") {
|
||||||
utils::logmesg(lmp,"\nFix style 'lb/pc' has been removed from the LATBOLTZ"
|
utils::logmesg(lmp,
|
||||||
" package; 'fix nve' can be used in its place.\n\n");
|
"\nFix style 'lb/pc' has been removed from the LATBOLTZ"
|
||||||
|
" package; 'fix nve' can be used in its place.\n\n");
|
||||||
} else if (my_style == "lb/rigid/pc/sphere") {
|
} else if (my_style == "lb/rigid/pc/sphere") {
|
||||||
utils::logmesg(lmp,"\nFix style 'lb/rigid/pc/sphere' has been removed from"
|
utils::logmesg(lmp,
|
||||||
|
"\nFix style 'lb/rigid/pc/sphere' has been removed from"
|
||||||
" the LATBOLTZ package; 'fix rigid' can be used in its place.\n\n");
|
" the LATBOLTZ package; 'fix rigid' can be used in its place.\n\n");
|
||||||
} else if (my_style == "client/md") {
|
} else if (my_style == "client/md") {
|
||||||
if (lmp->comm->me == 0)
|
if (lmp->comm->me == 0)
|
||||||
utils::logmesg(lmp, "\nThe MESSAGE package has been replaced by the MDI package.\n\n");
|
utils::logmesg(lmp, "\nThe MESSAGE package has been replaced by the MDI package.\n\n");
|
||||||
}
|
}
|
||||||
error->all(FLERR,"This fix style is no longer available");
|
error->all(FLERR, "This fix style is no longer available");
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -13,16 +12,16 @@
|
|||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#include "fix_dummy.h"
|
#include "fix_dummy.h"
|
||||||
#include <cstring>
|
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
|
||||||
|
#include <cstring>
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
using namespace FixConst;
|
using namespace FixConst;
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
FixDummy::FixDummy(LAMMPS *lmp, int narg, char **arg) :
|
FixDummy::FixDummy(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||||
Fix(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
// process optional args
|
// process optional args
|
||||||
// customize here and in setmask() by adding a new keyword from fix.h
|
// customize here and in setmask() by adding a new keyword from fix.h
|
||||||
@ -39,14 +38,22 @@ FixDummy::FixDummy(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
int iarg = 3;
|
int iarg = 3;
|
||||||
while (iarg < narg) {
|
while (iarg < narg) {
|
||||||
if (strcmp(arg[iarg],"initial_integrate") == 0) initial_integrate_flag = 1;
|
if (strcmp(arg[iarg], "initial_integrate") == 0)
|
||||||
else if (strcmp(arg[iarg],"final_integrate") == 0) final_integrate_flag = 1;
|
initial_integrate_flag = 1;
|
||||||
else if (strcmp(arg[iarg],"pre_exchange") == 0) pre_exchange_flag = 1;
|
else if (strcmp(arg[iarg], "final_integrate") == 0)
|
||||||
else if (strcmp(arg[iarg],"pre_neighbor") == 0) pre_neighbor_flag = 1;
|
final_integrate_flag = 1;
|
||||||
else if (strcmp(arg[iarg],"pre_force") == 0) pre_force_flag = 1;
|
else if (strcmp(arg[iarg], "pre_exchange") == 0)
|
||||||
else if (strcmp(arg[iarg],"post_force") == 0) post_force_flag = 1;
|
pre_exchange_flag = 1;
|
||||||
else if (strcmp(arg[iarg],"end_of_step") == 0) end_of_step_flag = 1;
|
else if (strcmp(arg[iarg], "pre_neighbor") == 0)
|
||||||
else error->all(FLERR,"Illegal fix DUMMY command");
|
pre_neighbor_flag = 1;
|
||||||
|
else if (strcmp(arg[iarg], "pre_force") == 0)
|
||||||
|
pre_force_flag = 1;
|
||||||
|
else if (strcmp(arg[iarg], "post_force") == 0)
|
||||||
|
post_force_flag = 1;
|
||||||
|
else if (strcmp(arg[iarg], "end_of_step") == 0)
|
||||||
|
end_of_step_flag = 1;
|
||||||
|
else
|
||||||
|
error->all(FLERR, "Illegal fix DUMMY command");
|
||||||
iarg++;
|
iarg++;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -22,13 +21,10 @@ using namespace FixConst;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) :
|
FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) : FixNH(lmp, narg, arg)
|
||||||
FixNH(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
if (tstat_flag)
|
if (tstat_flag) error->all(FLERR, "Temperature control can not be used with fix nph");
|
||||||
error->all(FLERR,"Temperature control can not be used with fix nph");
|
if (!pstat_flag) error->all(FLERR, "Pressure control must be used with fix nph");
|
||||||
if (!pstat_flag)
|
|
||||||
error->all(FLERR,"Pressure control must be used with fix nph");
|
|
||||||
|
|
||||||
// create a new compute temp style
|
// create a new compute temp style
|
||||||
// id = fix-ID + temp
|
// id = fix-ID + temp
|
||||||
@ -36,7 +32,7 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
// and thus its KE/temperature contribution should use group all
|
// and thus its KE/temperature contribution should use group all
|
||||||
|
|
||||||
id_temp = utils::strdup(std::string(id) + "_temp");
|
id_temp = utils::strdup(std::string(id) + "_temp");
|
||||||
modify->add_compute(fmt::format("{} all temp",id_temp));
|
modify->add_compute(fmt::format("{} all temp", id_temp));
|
||||||
tcomputeflag = 1;
|
tcomputeflag = 1;
|
||||||
|
|
||||||
// create a new compute pressure style
|
// create a new compute pressure style
|
||||||
@ -44,6 +40,6 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
// pass id_temp as 4th arg to pressure constructor
|
// pass id_temp as 4th arg to pressure constructor
|
||||||
|
|
||||||
id_press = utils::strdup(std::string(id) + "_press");
|
id_press = utils::strdup(std::string(id) + "_press");
|
||||||
modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp));
|
modify->add_compute(fmt::format("{} all pressure {}", id_press, id_temp));
|
||||||
pcomputeflag = 1;
|
pcomputeflag = 1;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -22,13 +21,10 @@ using namespace FixConst;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
FixNPHSphere::FixNPHSphere(LAMMPS *lmp, int narg, char **arg) :
|
FixNPHSphere::FixNPHSphere(LAMMPS *lmp, int narg, char **arg) : FixNHSphere(lmp, narg, arg)
|
||||||
FixNHSphere(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
if (tstat_flag)
|
if (tstat_flag) error->all(FLERR, "Temperature control can not be used with fix nph/sphere");
|
||||||
error->all(FLERR,"Temperature control can not be used with fix nph/sphere");
|
if (!pstat_flag) error->all(FLERR, "Pressure control must be used with fix nph/sphere");
|
||||||
if (!pstat_flag)
|
|
||||||
error->all(FLERR,"Pressure control must be used with fix nph/sphere");
|
|
||||||
|
|
||||||
// create a new compute temp style
|
// create a new compute temp style
|
||||||
// id = fix-ID + temp
|
// id = fix-ID + temp
|
||||||
@ -36,7 +32,7 @@ FixNPHSphere::FixNPHSphere(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
// and thus its KE/temperature contribution should use group all
|
// and thus its KE/temperature contribution should use group all
|
||||||
|
|
||||||
id_temp = utils::strdup(std::string(id) + "_temp");
|
id_temp = utils::strdup(std::string(id) + "_temp");
|
||||||
modify->add_compute(fmt::format("{} all temp/sphere",id_temp));
|
modify->add_compute(fmt::format("{} all temp/sphere", id_temp));
|
||||||
tcomputeflag = 1;
|
tcomputeflag = 1;
|
||||||
|
|
||||||
// create a new compute pressure style
|
// create a new compute pressure style
|
||||||
@ -44,6 +40,6 @@ FixNPHSphere::FixNPHSphere(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
// pass id_temp as 4th arg to pressure constructor
|
// pass id_temp as 4th arg to pressure constructor
|
||||||
|
|
||||||
id_press = utils::strdup(std::string(id) + "_press");
|
id_press = utils::strdup(std::string(id) + "_press");
|
||||||
modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp));
|
modify->add_compute(fmt::format("{} all pressure {}", id_press, id_temp));
|
||||||
pcomputeflag = 1;
|
pcomputeflag = 1;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -22,13 +21,10 @@ using namespace FixConst;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
|
FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) : FixNH(lmp, narg, arg)
|
||||||
FixNH(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
if (!tstat_flag)
|
if (!tstat_flag) error->all(FLERR, "Temperature control must be used with fix npt");
|
||||||
error->all(FLERR,"Temperature control must be used with fix npt");
|
if (!pstat_flag) error->all(FLERR, "Pressure control must be used with fix npt");
|
||||||
if (!pstat_flag)
|
|
||||||
error->all(FLERR,"Pressure control must be used with fix npt");
|
|
||||||
|
|
||||||
// create a new compute temp style
|
// create a new compute temp style
|
||||||
// id = fix-ID + temp
|
// id = fix-ID + temp
|
||||||
@ -36,7 +32,7 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
// and thus its KE/temperature contribution should use group all
|
// and thus its KE/temperature contribution should use group all
|
||||||
|
|
||||||
id_temp = utils::strdup(std::string(id) + "_temp");
|
id_temp = utils::strdup(std::string(id) + "_temp");
|
||||||
modify->add_compute(fmt::format("{} all temp",id_temp));
|
modify->add_compute(fmt::format("{} all temp", id_temp));
|
||||||
tcomputeflag = 1;
|
tcomputeflag = 1;
|
||||||
|
|
||||||
// create a new compute pressure style
|
// create a new compute pressure style
|
||||||
@ -44,6 +40,6 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
// pass id_temp as 4th arg to pressure constructor
|
// pass id_temp as 4th arg to pressure constructor
|
||||||
|
|
||||||
id_press = utils::strdup(std::string(id) + "_press");
|
id_press = utils::strdup(std::string(id) + "_press");
|
||||||
modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp));
|
modify->add_compute(fmt::format("{} all pressure {}", id_press, id_temp));
|
||||||
pcomputeflag = 1;
|
pcomputeflag = 1;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -22,13 +21,10 @@ using namespace FixConst;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) :
|
FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) : FixNHSphere(lmp, narg, arg)
|
||||||
FixNHSphere(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
if (!tstat_flag)
|
if (!tstat_flag) error->all(FLERR, "Temperature control must be used with fix npt/sphere");
|
||||||
error->all(FLERR,"Temperature control must be used with fix npt/sphere");
|
if (!pstat_flag) error->all(FLERR, "Pressure control must be used with fix npt/sphere");
|
||||||
if (!pstat_flag)
|
|
||||||
error->all(FLERR,"Pressure control must be used with fix npt/sphere");
|
|
||||||
|
|
||||||
// create a new compute temp style
|
// create a new compute temp style
|
||||||
// id = fix-ID + temp
|
// id = fix-ID + temp
|
||||||
@ -36,7 +32,7 @@ FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
// and thus its KE/temperature contribution should use group all
|
// and thus its KE/temperature contribution should use group all
|
||||||
|
|
||||||
id_temp = utils::strdup(std::string(id) + "_temp");
|
id_temp = utils::strdup(std::string(id) + "_temp");
|
||||||
modify->add_compute(fmt::format("{} all temp/sphere",id_temp));
|
modify->add_compute(fmt::format("{} all temp/sphere", id_temp));
|
||||||
tcomputeflag = 1;
|
tcomputeflag = 1;
|
||||||
|
|
||||||
// create a new compute pressure style
|
// create a new compute pressure style
|
||||||
@ -44,6 +40,6 @@ FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
// pass id_temp as 4th arg to pressure constructor
|
// pass id_temp as 4th arg to pressure constructor
|
||||||
|
|
||||||
id_press = utils::strdup(std::string(id) + "_press");
|
id_press = utils::strdup(std::string(id) + "_press");
|
||||||
modify->add_compute(fmt::format("{} all pressure {}",id_press, id_temp));
|
modify->add_compute(fmt::format("{} all pressure {}", id_press, id_temp));
|
||||||
pcomputeflag = 1;
|
pcomputeflag = 1;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -24,10 +23,9 @@ using namespace FixConst;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
FixNVENoforce::FixNVENoforce(LAMMPS *lmp, int narg, char **arg) :
|
FixNVENoforce::FixNVENoforce(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||||
Fix(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
if (narg != 3) error->all(FLERR,"Illegal fix nve/noforce command");
|
if (narg != 3) error->all(FLERR, "Illegal fix nve/noforce command");
|
||||||
|
|
||||||
time_integrate = 1;
|
time_integrate = 1;
|
||||||
}
|
}
|
||||||
@ -48,8 +46,8 @@ void FixNVENoforce::init()
|
|||||||
{
|
{
|
||||||
dtv = update->dt;
|
dtv = update->dt;
|
||||||
|
|
||||||
if (utils::strmatch(update->integrate_style,"^respa"))
|
if (utils::strmatch(update->integrate_style, "^respa"))
|
||||||
step_respa = (dynamic_cast<Respa *>( update->integrate))->step;
|
step_respa = (dynamic_cast<Respa *>(update->integrate))->step;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -75,7 +73,7 @@ void FixNVENoforce::initial_integrate(int /*vflag*/)
|
|||||||
|
|
||||||
void FixNVENoforce::initial_integrate_respa(int vflag, int ilevel, int flag)
|
void FixNVENoforce::initial_integrate_respa(int vflag, int ilevel, int flag)
|
||||||
{
|
{
|
||||||
if (flag) return; // only used by NPT,NPH
|
if (flag) return; // only used by NPT,NPH
|
||||||
|
|
||||||
dtv = step_respa[ilevel];
|
dtv = step_respa[ilevel];
|
||||||
|
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -23,18 +22,15 @@ using namespace FixConst;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) :
|
FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) : FixNH(lmp, narg, arg)
|
||||||
FixNH(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
if (!tstat_flag)
|
if (!tstat_flag) error->all(FLERR, "Temperature control must be used with fix nvt");
|
||||||
error->all(FLERR,"Temperature control must be used with fix nvt");
|
if (pstat_flag) error->all(FLERR, "Pressure control can not be used with fix nvt");
|
||||||
if (pstat_flag)
|
|
||||||
error->all(FLERR,"Pressure control can not be used with fix nvt");
|
|
||||||
|
|
||||||
// create a new compute temp style
|
// create a new compute temp style
|
||||||
// id = fix-ID + temp
|
// id = fix-ID + temp
|
||||||
|
|
||||||
id_temp = utils::strdup(std::string(id) + "_temp");
|
id_temp = utils::strdup(std::string(id) + "_temp");
|
||||||
modify->add_compute(fmt::format("{} {} temp",id_temp,group->names[igroup]));
|
modify->add_compute(fmt::format("{} {} temp", id_temp, group->names[igroup]));
|
||||||
tcomputeflag = 1;
|
tcomputeflag = 1;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -23,19 +22,15 @@ using namespace FixConst;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
FixNVTSphere::FixNVTSphere(LAMMPS *lmp, int narg, char **arg) :
|
FixNVTSphere::FixNVTSphere(LAMMPS *lmp, int narg, char **arg) : FixNHSphere(lmp, narg, arg)
|
||||||
FixNHSphere(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
if (!tstat_flag)
|
if (!tstat_flag) error->all(FLERR, "Temperature control must be used with fix nvt/sphere");
|
||||||
error->all(FLERR,"Temperature control must be used with fix nvt/sphere");
|
if (pstat_flag) error->all(FLERR, "Pressure control can not be used with fix nvt/sphere");
|
||||||
if (pstat_flag)
|
|
||||||
error->all(FLERR,"Pressure control can not be used with fix nvt/sphere");
|
|
||||||
|
|
||||||
// create a new compute temp style
|
// create a new compute temp style
|
||||||
// id = fix-ID + temp
|
// id = fix-ID + temp
|
||||||
|
|
||||||
id_temp = utils::strdup(std::string(id) + "_temp");
|
id_temp = utils::strdup(std::string(id) + "_temp");
|
||||||
modify->add_compute(fmt::format("{} {} temp/sphere",
|
modify->add_compute(fmt::format("{} {} temp/sphere", id_temp, group->names[igroup]));
|
||||||
id_temp,group->names[igroup]));
|
|
||||||
tcomputeflag = 1;
|
tcomputeflag = 1;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -21,8 +20,7 @@ using namespace FixConst;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
FixWallHarmonic::FixWallHarmonic(LAMMPS *lmp, int narg, char **arg) :
|
FixWallHarmonic::FixWallHarmonic(LAMMPS *lmp, int narg, char **arg) : FixWall(lmp, narg, arg)
|
||||||
FixWall(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
dynamic_group_allow = 1;
|
dynamic_group_allow = 1;
|
||||||
}
|
}
|
||||||
@ -36,7 +34,7 @@ FixWallHarmonic::FixWallHarmonic(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
void FixWallHarmonic::wall_particle(int m, int which, double coord)
|
void FixWallHarmonic::wall_particle(int m, int which, double coord)
|
||||||
{
|
{
|
||||||
double delta,dr,fwall;
|
double delta, dr, fwall;
|
||||||
double vn;
|
double vn;
|
||||||
|
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
@ -52,25 +50,29 @@ void FixWallHarmonic::wall_particle(int m, int which, double coord)
|
|||||||
|
|
||||||
for (int i = 0; i < nlocal; i++)
|
for (int i = 0; i < nlocal; i++)
|
||||||
if (mask[i] & groupbit) {
|
if (mask[i] & groupbit) {
|
||||||
if (side < 0) delta = x[i][dim] - coord;
|
if (side < 0)
|
||||||
else delta = coord - x[i][dim];
|
delta = x[i][dim] - coord;
|
||||||
|
else
|
||||||
|
delta = coord - x[i][dim];
|
||||||
if (delta >= cutoff[m]) continue;
|
if (delta >= cutoff[m]) continue;
|
||||||
if (delta <= 0.0) {
|
if (delta <= 0.0) {
|
||||||
onflag = 1;
|
onflag = 1;
|
||||||
continue;
|
continue;
|
||||||
}
|
}
|
||||||
dr = cutoff[m]-delta;
|
dr = cutoff[m] - delta;
|
||||||
fwall = side * 2.0*epsilon[m]*dr;
|
fwall = side * 2.0 * epsilon[m] * dr;
|
||||||
f[i][dim] -= fwall;
|
f[i][dim] -= fwall;
|
||||||
ewall[0] += epsilon[m]*dr*dr;
|
ewall[0] += epsilon[m] * dr * dr;
|
||||||
ewall[m+1] += fwall;
|
ewall[m + 1] += fwall;
|
||||||
|
|
||||||
if (evflag) {
|
if (evflag) {
|
||||||
if (side < 0) vn = -fwall*delta;
|
if (side < 0)
|
||||||
else vn = fwall*delta;
|
vn = -fwall * delta;
|
||||||
v_tally(dim,i,vn);
|
else
|
||||||
|
vn = fwall * delta;
|
||||||
|
v_tally(dim, i, vn);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
if (onflag) error->one(FLERR,"Particle on or inside fix wall surface");
|
if (onflag) error->one(FLERR, "Particle on or inside fix wall surface");
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -13,17 +12,17 @@
|
|||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#include "fix_wall_morse.h"
|
#include "fix_wall_morse.h"
|
||||||
#include <cmath>
|
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
|
||||||
|
#include <cmath>
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
using namespace FixConst;
|
using namespace FixConst;
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
FixWallMorse::FixWallMorse(LAMMPS *lmp, int narg, char **arg) :
|
FixWallMorse::FixWallMorse(LAMMPS *lmp, int narg, char **arg) : FixWall(lmp, narg, arg)
|
||||||
FixWall(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
dynamic_group_allow = 1;
|
dynamic_group_allow = 1;
|
||||||
}
|
}
|
||||||
@ -34,7 +33,7 @@ void FixWallMorse::precompute(int m)
|
|||||||
{
|
{
|
||||||
coeff1[m] = 2.0 * epsilon[m] * alpha[m];
|
coeff1[m] = 2.0 * epsilon[m] * alpha[m];
|
||||||
const double alpha_dr = -alpha[m] * (cutoff[m] - sigma[m]);
|
const double alpha_dr = -alpha[m] * (cutoff[m] - sigma[m]);
|
||||||
offset[m] = epsilon[m] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
|
offset[m] = epsilon[m] * (exp(2.0 * alpha_dr) - 2.0 * exp(alpha_dr));
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -46,7 +45,7 @@ void FixWallMorse::precompute(int m)
|
|||||||
|
|
||||||
void FixWallMorse::wall_particle(int m, int which, double coord)
|
void FixWallMorse::wall_particle(int m, int which, double coord)
|
||||||
{
|
{
|
||||||
double delta,fwall;
|
double delta, fwall;
|
||||||
double vn;
|
double vn;
|
||||||
|
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
@ -62,8 +61,10 @@ void FixWallMorse::wall_particle(int m, int which, double coord)
|
|||||||
|
|
||||||
for (int i = 0; i < nlocal; i++) {
|
for (int i = 0; i < nlocal; i++) {
|
||||||
if (mask[i] & groupbit) {
|
if (mask[i] & groupbit) {
|
||||||
if (side < 0) delta = x[i][dim] - coord;
|
if (side < 0)
|
||||||
else delta = coord - x[i][dim];
|
delta = x[i][dim] - coord;
|
||||||
|
else
|
||||||
|
delta = coord - x[i][dim];
|
||||||
if (delta >= cutoff[m]) continue;
|
if (delta >= cutoff[m]) continue;
|
||||||
if (delta <= 0.0) {
|
if (delta <= 0.0) {
|
||||||
onflag = 1;
|
onflag = 1;
|
||||||
@ -71,18 +72,20 @@ void FixWallMorse::wall_particle(int m, int which, double coord)
|
|||||||
}
|
}
|
||||||
double dr = delta - sigma[m];
|
double dr = delta - sigma[m];
|
||||||
double dexp = exp(-alpha[m] * dr);
|
double dexp = exp(-alpha[m] * dr);
|
||||||
fwall = side * coeff1[m] * (dexp*dexp - dexp) / delta;
|
fwall = side * coeff1[m] * (dexp * dexp - dexp) / delta;
|
||||||
ewall[0] += epsilon[m] * (dexp*dexp - 2.0*dexp) - offset[m];
|
ewall[0] += epsilon[m] * (dexp * dexp - 2.0 * dexp) - offset[m];
|
||||||
f[i][dim] -= fwall;
|
f[i][dim] -= fwall;
|
||||||
ewall[m+1] += fwall;
|
ewall[m + 1] += fwall;
|
||||||
|
|
||||||
if (evflag) {
|
if (evflag) {
|
||||||
if (side < 0) vn = -fwall*delta;
|
if (side < 0)
|
||||||
else vn = fwall*delta;
|
vn = -fwall * delta;
|
||||||
|
else
|
||||||
|
vn = fwall * delta;
|
||||||
v_tally(dim, i, vn);
|
v_tally(dim, i, vn);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
if (onflag) error->one(FLERR,"Particle on or inside fix wall surface");
|
if (onflag) error->one(FLERR, "Particle on or inside fix wall surface");
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -19,8 +18,8 @@
|
|||||||
#include "kspace_deprecated.h"
|
#include "kspace_deprecated.h"
|
||||||
|
|
||||||
#include "comm.h"
|
#include "comm.h"
|
||||||
#include "force.h"
|
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
#include "force.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -31,11 +30,8 @@ void KSpaceDeprecated::settings(int, char **)
|
|||||||
std::string my_style = force->kspace_style;
|
std::string my_style = force->kspace_style;
|
||||||
|
|
||||||
if (my_style == "DEPRECATED") {
|
if (my_style == "DEPRECATED") {
|
||||||
if (lmp->comm->me == 0)
|
if (lmp->comm->me == 0) utils::logmesg(lmp, "\nKSpace style 'DEPRECATED' is a dummy style\n\n");
|
||||||
utils::logmesg(lmp,"\nKSpace style 'DEPRECATED' is a dummy style\n\n");
|
|
||||||
return;
|
return;
|
||||||
}
|
}
|
||||||
error->all(FLERR,"This kspace style is no longer available");
|
error->all(FLERR, "This kspace style is no longer available");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -32,28 +31,26 @@ Minimize::Minimize(LAMMPS *lmp) : Command(lmp) {}
|
|||||||
|
|
||||||
void Minimize::command(int narg, char **arg)
|
void Minimize::command(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (narg != 4) error->all(FLERR,"Illegal minimize command");
|
if (narg != 4) error->all(FLERR, "Illegal minimize command");
|
||||||
|
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,"Minimize command before simulation box is defined");
|
error->all(FLERR, "Minimize command before simulation box is defined");
|
||||||
|
|
||||||
// ignore minimize command, if walltime limit was already reached
|
// ignore minimize command, if walltime limit was already reached
|
||||||
if (timer->is_timeout()) return;
|
if (timer->is_timeout()) return;
|
||||||
|
|
||||||
update->etol = utils::numeric(FLERR,arg[0],false,lmp);
|
update->etol = utils::numeric(FLERR, arg[0], false, lmp);
|
||||||
update->ftol = utils::numeric(FLERR,arg[1],false,lmp);
|
update->ftol = utils::numeric(FLERR, arg[1], false, lmp);
|
||||||
update->nsteps = utils::inumeric(FLERR,arg[2],false,lmp);
|
update->nsteps = utils::inumeric(FLERR, arg[2], false, lmp);
|
||||||
update->max_eval = utils::inumeric(FLERR,arg[3],false,lmp);
|
update->max_eval = utils::inumeric(FLERR, arg[3], false, lmp);
|
||||||
|
|
||||||
if (update->etol < 0.0 || update->ftol < 0.0)
|
if (update->etol < 0.0 || update->ftol < 0.0) error->all(FLERR, "Illegal minimize command");
|
||||||
error->all(FLERR,"Illegal minimize command");
|
|
||||||
|
|
||||||
if (lmp->citeme) lmp->citeme->flush();
|
if (lmp->citeme) lmp->citeme->flush();
|
||||||
update->whichflag = 2;
|
update->whichflag = 2;
|
||||||
update->beginstep = update->firststep = update->ntimestep;
|
update->beginstep = update->firststep = update->ntimestep;
|
||||||
update->endstep = update->laststep = update->firststep + update->nsteps;
|
update->endstep = update->laststep = update->firststep + update->nsteps;
|
||||||
if (update->laststep < 0)
|
if (update->laststep < 0) error->all(FLERR, "Too many iterations");
|
||||||
error->all(FLERR,"Too many iterations");
|
|
||||||
|
|
||||||
lmp->init();
|
lmp->init();
|
||||||
timer->init_timeout();
|
timer->init_timeout();
|
||||||
|
|||||||
@ -1742,15 +1742,15 @@ void Neighbor::requests_new2old()
|
|||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
find and return request made by classptr
|
find and return request made by classptr
|
||||||
if not found or classptr = nullptr, return nullptr
|
if not found or classptr = nullptr, return nullptr
|
||||||
TODO: should have optional argument "id" to match ID if multiple requests
|
id is optional and defaults to 0, which is the request id value unless set explicitly
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
NeighRequest *Neighbor::find_request(void *classptr) const
|
NeighRequest *Neighbor::find_request(void *classptr, const int id) const
|
||||||
{
|
{
|
||||||
if (classptr == nullptr) return nullptr;
|
if (classptr == nullptr) return nullptr;
|
||||||
|
|
||||||
for (int i = 0; i < nrequest; i++)
|
for (int i = 0; i < nrequest; i++)
|
||||||
if (requests[i]->requestor == classptr) return requests[i];
|
if ((requests[i]->requestor == classptr) && (requests[i]->id == id)) return requests[i];
|
||||||
|
|
||||||
return nullptr;
|
return nullptr;
|
||||||
}
|
}
|
||||||
@ -1770,15 +1770,15 @@ const std::vector<NeighRequest *> Neighbor::get_pair_requests() const
|
|||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
find and return list requested by classptr
|
find and return list requested by classptr
|
||||||
if not found or classptr = nullptr, return nullptr
|
if not found or classptr = nullptr, return nullptr
|
||||||
TODO: should have optional argument "id" to match ID if multiple requests
|
id is optional and defaults to 0, which is the request id value unless set explicitly
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
NeighList *Neighbor::find_list(void *classptr) const
|
NeighList *Neighbor::find_list(void *classptr, const int id) const
|
||||||
{
|
{
|
||||||
if (classptr == nullptr) return nullptr;
|
if (classptr == nullptr) return nullptr;
|
||||||
|
|
||||||
for (int i = 0; i < nlist; i++)
|
for (int i = 0; i < nlist; i++)
|
||||||
if (lists[i]->requestor == classptr) return lists[i];
|
if ((lists[i]->requestor == classptr) && (lists[i]->id == id)) return lists[i];
|
||||||
|
|
||||||
return nullptr;
|
return nullptr;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -153,8 +153,12 @@ class Neighbor : protected Pointers {
|
|||||||
|
|
||||||
void exclusion_group_group_delete(int, int); // rm a group-group exclusion
|
void exclusion_group_group_delete(int, int); // rm a group-group exclusion
|
||||||
int exclude_setting(); // return exclude value to accelerator pkg
|
int exclude_setting(); // return exclude value to accelerator pkg
|
||||||
NeighList *find_list(void *) const; // find a neighbor list based on requestor
|
|
||||||
NeighRequest *find_request(void *) const; // find a neighbor request based on requestor
|
// find a neighbor list based on requestor
|
||||||
|
NeighList *find_list(void *, const int id = 0) const;
|
||||||
|
// find a neighbor request based on requestor
|
||||||
|
NeighRequest *find_request(void *, const int id = 0) const;
|
||||||
|
|
||||||
const std::vector<NeighRequest *> get_pair_requests() const;
|
const std::vector<NeighRequest *> get_pair_requests() const;
|
||||||
int any_full(); // Check if any old requests had full neighbor lists
|
int any_full(); // Check if any old requests had full neighbor lists
|
||||||
void build_collection(int); // build peratom collection array starting at the given index
|
void build_collection(int); // build peratom collection array starting at the given index
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -32,8 +31,8 @@ NPairFullBinAtomonly::NPairFullBinAtomonly(LAMMPS *lmp) : NPair(lmp) {}
|
|||||||
|
|
||||||
void NPairFullBinAtomonly::build(NeighList *list)
|
void NPairFullBinAtomonly::build(NeighList *list)
|
||||||
{
|
{
|
||||||
int i,j,k,n,itype,jtype,ibin;
|
int i, j, k, n, itype, jtype, ibin;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
|
||||||
int *neighptr;
|
int *neighptr;
|
||||||
|
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
@ -66,16 +65,16 @@ void NPairFullBinAtomonly::build(NeighList *list)
|
|||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
|
|
||||||
for (k = 0; k < nstencil; k++) {
|
for (k = 0; k < nstencil; k++) {
|
||||||
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
|
for (j = binhead[ibin + stencil[k]]; j >= 0; j = bins[j]) {
|
||||||
if (i == j) continue;
|
if (i == j) continue;
|
||||||
|
|
||||||
jtype = type[j];
|
jtype = type[j];
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
if (exclude && exclusion(i, j, itype, jtype, mask, molecule)) continue;
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
delx = xtmp - x[j][0];
|
||||||
dely = ytmp - x[j][1];
|
dely = ytmp - x[j][1];
|
||||||
delz = ztmp - x[j][2];
|
delz = ztmp - x[j][2];
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
rsq = delx * delx + dely * dely + delz * delz;
|
||||||
|
|
||||||
if (rsq <= cutneighsq[itype][jtype]) neighptr[n++] = j;
|
if (rsq <= cutneighsq[itype][jtype]) neighptr[n++] = j;
|
||||||
}
|
}
|
||||||
@ -85,8 +84,7 @@ void NPairFullBinAtomonly::build(NeighList *list)
|
|||||||
firstneigh[i] = neighptr;
|
firstneigh[i] = neighptr;
|
||||||
numneigh[i] = n;
|
numneigh[i] = n;
|
||||||
ipage->vgot(n);
|
ipage->vgot(n);
|
||||||
if (ipage->status())
|
if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
|
||||||
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
|
||||||
}
|
}
|
||||||
|
|
||||||
list->inum = inum;
|
list->inum = inum;
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -35,8 +34,8 @@ NPairHalffullNewtoff::NPairHalffullNewtoff(LAMMPS *lmp) : NPair(lmp) {}
|
|||||||
|
|
||||||
void NPairHalffullNewtoff::build(NeighList *list)
|
void NPairHalffullNewtoff::build(NeighList *list)
|
||||||
{
|
{
|
||||||
int i,j,ii,jj,n,jnum,joriginal;
|
int i, j, ii, jj, n, jnum, joriginal;
|
||||||
int *neighptr,*jlist;
|
int *neighptr, *jlist;
|
||||||
|
|
||||||
int *ilist = list->ilist;
|
int *ilist = list->ilist;
|
||||||
int *numneigh = list->numneigh;
|
int *numneigh = list->numneigh;
|
||||||
@ -74,8 +73,7 @@ void NPairHalffullNewtoff::build(NeighList *list)
|
|||||||
firstneigh[i] = neighptr;
|
firstneigh[i] = neighptr;
|
||||||
numneigh[i] = n;
|
numneigh[i] = n;
|
||||||
ipage->vgot(n);
|
ipage->vgot(n);
|
||||||
if (ipage->status())
|
if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
|
||||||
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
|
||||||
}
|
}
|
||||||
|
|
||||||
list->inum = inum;
|
list->inum = inum;
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -32,8 +31,8 @@ NPairSkipSize::NPairSkipSize(LAMMPS *lmp) : NPair(lmp) {}
|
|||||||
|
|
||||||
void NPairSkipSize::build(NeighList *list)
|
void NPairSkipSize::build(NeighList *list)
|
||||||
{
|
{
|
||||||
int i,j,ii,jj,n,itype,jnum,joriginal;
|
int i, j, ii, jj, n, itype, jnum, joriginal;
|
||||||
int *neighptr,*jlist;
|
int *neighptr, *jlist;
|
||||||
|
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
int *ilist = list->ilist;
|
int *ilist = list->ilist;
|
||||||
@ -80,8 +79,7 @@ void NPairSkipSize::build(NeighList *list)
|
|||||||
firstneigh[i] = neighptr;
|
firstneigh[i] = neighptr;
|
||||||
numneigh[i] = n;
|
numneigh[i] = n;
|
||||||
ipage->vgot(n);
|
ipage->vgot(n);
|
||||||
if (ipage->status())
|
if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
|
||||||
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
|
||||||
}
|
}
|
||||||
|
|
||||||
list->inum = inum;
|
list->inum = inum;
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -26,12 +25,11 @@ NStencilFullBin2d::NStencilFullBin2d(LAMMPS *lmp) : NStencil(lmp) {}
|
|||||||
|
|
||||||
void NStencilFullBin2d::create()
|
void NStencilFullBin2d::create()
|
||||||
{
|
{
|
||||||
int i,j;
|
int i, j;
|
||||||
|
|
||||||
nstencil = 0;
|
nstencil = 0;
|
||||||
|
|
||||||
for (j = -sy; j <= sy; j++)
|
for (j = -sy; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++)
|
for (i = -sx; i <= sx; i++)
|
||||||
if (bin_distance(i,j,0) < cutneighmaxsq)
|
if (bin_distance(i, j, 0) < cutneighmaxsq) stencil[nstencil++] = j * mbinx + i;
|
||||||
stencil[nstencil++] = j*mbinx + i;
|
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -26,13 +25,13 @@ NStencilFullBin3d::NStencilFullBin3d(LAMMPS *lmp) : NStencil(lmp) {}
|
|||||||
|
|
||||||
void NStencilFullBin3d::create()
|
void NStencilFullBin3d::create()
|
||||||
{
|
{
|
||||||
int i,j,k;
|
int i, j, k;
|
||||||
|
|
||||||
nstencil = 0;
|
nstencil = 0;
|
||||||
|
|
||||||
for (k = -sz; k <= sz; k++)
|
for (k = -sz; k <= sz; k++)
|
||||||
for (j = -sy; j <= sy; j++)
|
for (j = -sy; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++)
|
for (i = -sx; i <= sx; i++)
|
||||||
if (bin_distance(i,j,k) < cutneighmaxsq)
|
if (bin_distance(i, j, k) < cutneighmaxsq)
|
||||||
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
|
stencil[nstencil++] = k * mbiny * mbinx + j * mbinx + i;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -29,16 +28,16 @@ NStencilFullGhostBin2d::NStencilFullGhostBin2d(LAMMPS *lmp) : NStencil(lmp)
|
|||||||
|
|
||||||
void NStencilFullGhostBin2d::create()
|
void NStencilFullGhostBin2d::create()
|
||||||
{
|
{
|
||||||
int i,j;
|
int i, j;
|
||||||
|
|
||||||
nstencil = 0;
|
nstencil = 0;
|
||||||
|
|
||||||
for (j = -sy; j <= sy; j++)
|
for (j = -sy; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++)
|
for (i = -sx; i <= sx; i++)
|
||||||
if (bin_distance(i,j,0) < cutneighmaxsq) {
|
if (bin_distance(i, j, 0) < cutneighmaxsq) {
|
||||||
stencilxyz[nstencil][0] = i;
|
stencilxyz[nstencil][0] = i;
|
||||||
stencilxyz[nstencil][1] = j;
|
stencilxyz[nstencil][1] = j;
|
||||||
stencilxyz[nstencil][2] = 0;
|
stencilxyz[nstencil][2] = 0;
|
||||||
stencil[nstencil++] = j*mbinx + i;
|
stencil[nstencil++] = j * mbinx + i;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -29,17 +28,17 @@ NStencilFullGhostBin3d::NStencilFullGhostBin3d(LAMMPS *lmp) : NStencil(lmp)
|
|||||||
|
|
||||||
void NStencilFullGhostBin3d::create()
|
void NStencilFullGhostBin3d::create()
|
||||||
{
|
{
|
||||||
int i,j,k;
|
int i, j, k;
|
||||||
|
|
||||||
nstencil = 0;
|
nstencil = 0;
|
||||||
|
|
||||||
for (k = -sz; k <= sz; k++)
|
for (k = -sz; k <= sz; k++)
|
||||||
for (j = -sy; j <= sy; j++)
|
for (j = -sy; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++)
|
for (i = -sx; i <= sx; i++)
|
||||||
if (bin_distance(i,j,k) < cutneighmaxsq) {
|
if (bin_distance(i, j, k) < cutneighmaxsq) {
|
||||||
stencilxyz[nstencil][0] = i;
|
stencilxyz[nstencil][0] = i;
|
||||||
stencilxyz[nstencil][1] = j;
|
stencilxyz[nstencil][1] = j;
|
||||||
stencilxyz[nstencil][2] = k;
|
stencilxyz[nstencil][2] = k;
|
||||||
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
|
stencil[nstencil++] = k * mbiny * mbinx + j * mbinx + i;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -50,7 +49,6 @@ void NStencilFullMulti2d::create()
|
|||||||
int n = ncollections;
|
int n = ncollections;
|
||||||
double cutsq;
|
double cutsq;
|
||||||
|
|
||||||
|
|
||||||
for (icollection = 0; icollection < n; icollection++) {
|
for (icollection = 0; icollection < n; icollection++) {
|
||||||
for (jcollection = 0; jcollection < n; jcollection++) {
|
for (jcollection = 0; jcollection < n; jcollection++) {
|
||||||
if (flag_skip_multi[icollection][jcollection]) {
|
if (flag_skip_multi[icollection][jcollection]) {
|
||||||
@ -72,8 +70,8 @@ void NStencilFullMulti2d::create()
|
|||||||
|
|
||||||
for (j = -sy; j <= sy; j++)
|
for (j = -sy; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++)
|
for (i = -sx; i <= sx; i++)
|
||||||
if (bin_distance_multi(i,j,0,bin_collection) < cutsq)
|
if (bin_distance_multi(i, j, 0, bin_collection) < cutsq)
|
||||||
stencil_multi[icollection][jcollection][ns++] = j*mbinx + i;
|
stencil_multi[icollection][jcollection][ns++] = j * mbinx + i;
|
||||||
|
|
||||||
nstencil_multi[icollection][jcollection] = ns;
|
nstencil_multi[icollection][jcollection] = ns;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -27,8 +26,8 @@ NStencilFullMultiOld2d::NStencilFullMultiOld2d(LAMMPS *lmp) : NStencil(lmp) {}
|
|||||||
|
|
||||||
void NStencilFullMultiOld2d::create()
|
void NStencilFullMultiOld2d::create()
|
||||||
{
|
{
|
||||||
int i,j,n;
|
int i, j, n;
|
||||||
double rsq,typesq;
|
double rsq, typesq;
|
||||||
int *s;
|
int *s;
|
||||||
double *distsq;
|
double *distsq;
|
||||||
|
|
||||||
@ -40,10 +39,10 @@ void NStencilFullMultiOld2d::create()
|
|||||||
n = 0;
|
n = 0;
|
||||||
for (j = -sy; j <= sy; j++)
|
for (j = -sy; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++) {
|
for (i = -sx; i <= sx; i++) {
|
||||||
rsq = bin_distance(i,j,0);
|
rsq = bin_distance(i, j, 0);
|
||||||
if (rsq < typesq) {
|
if (rsq < typesq) {
|
||||||
distsq[n] = rsq;
|
distsq[n] = rsq;
|
||||||
s[n++] = j*mbinx + i;
|
s[n++] = j * mbinx + i;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
nstencil_multi_old[itype] = n;
|
nstencil_multi_old[itype] = n;
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -27,8 +26,8 @@ NStencilFullMultiOld3d::NStencilFullMultiOld3d(LAMMPS *lmp) : NStencil(lmp) {}
|
|||||||
|
|
||||||
void NStencilFullMultiOld3d::create()
|
void NStencilFullMultiOld3d::create()
|
||||||
{
|
{
|
||||||
int i,j,k,n;
|
int i, j, k, n;
|
||||||
double rsq,typesq;
|
double rsq, typesq;
|
||||||
int *s;
|
int *s;
|
||||||
double *distsq;
|
double *distsq;
|
||||||
|
|
||||||
@ -41,10 +40,10 @@ void NStencilFullMultiOld3d::create()
|
|||||||
for (k = -sz; k <= sz; k++)
|
for (k = -sz; k <= sz; k++)
|
||||||
for (j = -sy; j <= sy; j++)
|
for (j = -sy; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++) {
|
for (i = -sx; i <= sx; i++) {
|
||||||
rsq = bin_distance(i,j,k);
|
rsq = bin_distance(i, j, k);
|
||||||
if (rsq < typesq) {
|
if (rsq < typesq) {
|
||||||
distsq[n] = rsq;
|
distsq[n] = rsq;
|
||||||
s[n++] = k*mbiny*mbinx + j*mbinx + i;
|
s[n++] = k * mbiny * mbinx + j * mbinx + i;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
nstencil_multi_old[itype] = n;
|
nstencil_multi_old[itype] = n;
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -26,13 +25,12 @@ NStencilHalfBin2d::NStencilHalfBin2d(LAMMPS *lmp) : NStencil(lmp) {}
|
|||||||
|
|
||||||
void NStencilHalfBin2d::create()
|
void NStencilHalfBin2d::create()
|
||||||
{
|
{
|
||||||
int i,j;
|
int i, j;
|
||||||
|
|
||||||
nstencil = 0;
|
nstencil = 0;
|
||||||
|
|
||||||
for (j = 0; j <= sy; j++)
|
for (j = 0; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++)
|
for (i = -sx; i <= sx; i++)
|
||||||
if (j > 0 || (j == 0 && i > 0))
|
if (j > 0 || (j == 0 && i > 0))
|
||||||
if (bin_distance(i,j,0) < cutneighmaxsq)
|
if (bin_distance(i, j, 0) < cutneighmaxsq) stencil[nstencil++] = j * mbinx + i;
|
||||||
stencil[nstencil++] = j*mbinx + i;
|
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -18,8 +17,7 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
NStencilHalfBin2dTri::NStencilHalfBin2dTri(LAMMPS *lmp) :
|
NStencilHalfBin2dTri::NStencilHalfBin2dTri(LAMMPS *lmp) : NStencil(lmp) {}
|
||||||
NStencil(lmp) {}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
create stencil based on bin geometry and cutoff
|
create stencil based on bin geometry and cutoff
|
||||||
@ -27,12 +25,11 @@ NStencilHalfBin2dTri::NStencilHalfBin2dTri(LAMMPS *lmp) :
|
|||||||
|
|
||||||
void NStencilHalfBin2dTri::create()
|
void NStencilHalfBin2dTri::create()
|
||||||
{
|
{
|
||||||
int i,j;
|
int i, j;
|
||||||
|
|
||||||
nstencil = 0;
|
nstencil = 0;
|
||||||
|
|
||||||
for (j = 0; j <= sy; j++)
|
for (j = 0; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++)
|
for (i = -sx; i <= sx; i++)
|
||||||
if (bin_distance(i,j,0) < cutneighmaxsq)
|
if (bin_distance(i, j, 0) < cutneighmaxsq) stencil[nstencil++] = j * mbinx + i;
|
||||||
stencil[nstencil++] = j*mbinx + i;
|
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -26,7 +25,7 @@ NStencilHalfBin3d::NStencilHalfBin3d(LAMMPS *lmp) : NStencil(lmp) {}
|
|||||||
|
|
||||||
void NStencilHalfBin3d::create()
|
void NStencilHalfBin3d::create()
|
||||||
{
|
{
|
||||||
int i,j,k;
|
int i, j, k;
|
||||||
|
|
||||||
nstencil = 0;
|
nstencil = 0;
|
||||||
|
|
||||||
@ -34,6 +33,6 @@ void NStencilHalfBin3d::create()
|
|||||||
for (j = -sy; j <= sy; j++)
|
for (j = -sy; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++)
|
for (i = -sx; i <= sx; i++)
|
||||||
if (k > 0 || j > 0 || (j == 0 && i > 0))
|
if (k > 0 || j > 0 || (j == 0 && i > 0))
|
||||||
if (bin_distance(i,j,k) < cutneighmaxsq)
|
if (bin_distance(i, j, k) < cutneighmaxsq)
|
||||||
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
|
stencil[nstencil++] = k * mbiny * mbinx + j * mbinx + i;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -18,8 +17,7 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
NStencilHalfBin3dTri::NStencilHalfBin3dTri(LAMMPS *lmp) :
|
NStencilHalfBin3dTri::NStencilHalfBin3dTri(LAMMPS *lmp) : NStencil(lmp) {}
|
||||||
NStencil(lmp) {}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
create stencil based on bin geometry and cutoff
|
create stencil based on bin geometry and cutoff
|
||||||
@ -27,13 +25,13 @@ NStencilHalfBin3dTri::NStencilHalfBin3dTri(LAMMPS *lmp) :
|
|||||||
|
|
||||||
void NStencilHalfBin3dTri::create()
|
void NStencilHalfBin3dTri::create()
|
||||||
{
|
{
|
||||||
int i,j,k;
|
int i, j, k;
|
||||||
|
|
||||||
nstencil = 0;
|
nstencil = 0;
|
||||||
|
|
||||||
for (k = 0; k <= sz; k++)
|
for (k = 0; k <= sz; k++)
|
||||||
for (j = -sy; j <= sy; j++)
|
for (j = -sy; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++)
|
for (i = -sx; i <= sx; i++)
|
||||||
if (bin_distance(i,j,k) < cutneighmaxsq)
|
if (bin_distance(i, j, k) < cutneighmaxsq)
|
||||||
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
|
stencil[nstencil++] = k * mbiny * mbinx + j * mbinx + i;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -19,8 +18,7 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
NStencilHalfMultiOld2d::
|
NStencilHalfMultiOld2d::NStencilHalfMultiOld2d(LAMMPS *lmp) : NStencil(lmp) {}
|
||||||
NStencilHalfMultiOld2d(LAMMPS *lmp) : NStencil(lmp) {}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
create stencil based on bin geometry and cutoff
|
create stencil based on bin geometry and cutoff
|
||||||
@ -28,8 +26,8 @@ NStencilHalfMultiOld2d(LAMMPS *lmp) : NStencil(lmp) {}
|
|||||||
|
|
||||||
void NStencilHalfMultiOld2d::create()
|
void NStencilHalfMultiOld2d::create()
|
||||||
{
|
{
|
||||||
int i,j,n;
|
int i, j, n;
|
||||||
double rsq,typesq;
|
double rsq, typesq;
|
||||||
int *s;
|
int *s;
|
||||||
double *distsq;
|
double *distsq;
|
||||||
|
|
||||||
@ -42,10 +40,10 @@ void NStencilHalfMultiOld2d::create()
|
|||||||
for (j = 0; j <= sy; j++)
|
for (j = 0; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++)
|
for (i = -sx; i <= sx; i++)
|
||||||
if (j > 0 || (j == 0 && i > 0)) {
|
if (j > 0 || (j == 0 && i > 0)) {
|
||||||
rsq = bin_distance(i,j,0);
|
rsq = bin_distance(i, j, 0);
|
||||||
if (rsq < typesq) {
|
if (rsq < typesq) {
|
||||||
distsq[n] = rsq;
|
distsq[n] = rsq;
|
||||||
s[n++] = j*mbinx + i;
|
s[n++] = j * mbinx + i;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
nstencil_multi_old[itype] = n;
|
nstencil_multi_old[itype] = n;
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -19,8 +18,7 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
NStencilHalfMultiOld2dTri::
|
NStencilHalfMultiOld2dTri::NStencilHalfMultiOld2dTri(LAMMPS *lmp) : NStencil(lmp) {}
|
||||||
NStencilHalfMultiOld2dTri(LAMMPS *lmp) : NStencil(lmp) {}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
create stencil based on bin geometry and cutoff
|
create stencil based on bin geometry and cutoff
|
||||||
@ -28,8 +26,8 @@ NStencilHalfMultiOld2dTri(LAMMPS *lmp) : NStencil(lmp) {}
|
|||||||
|
|
||||||
void NStencilHalfMultiOld2dTri::create()
|
void NStencilHalfMultiOld2dTri::create()
|
||||||
{
|
{
|
||||||
int i,j,n;
|
int i, j, n;
|
||||||
double rsq,typesq;
|
double rsq, typesq;
|
||||||
int *s;
|
int *s;
|
||||||
double *distsq;
|
double *distsq;
|
||||||
|
|
||||||
@ -41,10 +39,10 @@ void NStencilHalfMultiOld2dTri::create()
|
|||||||
n = 0;
|
n = 0;
|
||||||
for (j = 0; j <= sy; j++)
|
for (j = 0; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++) {
|
for (i = -sx; i <= sx; i++) {
|
||||||
rsq = bin_distance(i,j,0);
|
rsq = bin_distance(i, j, 0);
|
||||||
if (rsq < typesq) {
|
if (rsq < typesq) {
|
||||||
distsq[n] = rsq;
|
distsq[n] = rsq;
|
||||||
s[n++] = j*mbinx + i;
|
s[n++] = j * mbinx + i;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
nstencil_multi_old[itype] = n;
|
nstencil_multi_old[itype] = n;
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -19,8 +18,7 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
NStencilHalfMultiOld3d::
|
NStencilHalfMultiOld3d::NStencilHalfMultiOld3d(LAMMPS *lmp) : NStencil(lmp) {}
|
||||||
NStencilHalfMultiOld3d(LAMMPS *lmp) : NStencil(lmp) {}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
create stencil based on bin geometry and cutoff
|
create stencil based on bin geometry and cutoff
|
||||||
@ -28,8 +26,8 @@ NStencilHalfMultiOld3d(LAMMPS *lmp) : NStencil(lmp) {}
|
|||||||
|
|
||||||
void NStencilHalfMultiOld3d::create()
|
void NStencilHalfMultiOld3d::create()
|
||||||
{
|
{
|
||||||
int i,j,k,n;
|
int i, j, k, n;
|
||||||
double rsq,typesq;
|
double rsq, typesq;
|
||||||
int *s;
|
int *s;
|
||||||
double *distsq;
|
double *distsq;
|
||||||
|
|
||||||
@ -43,10 +41,10 @@ void NStencilHalfMultiOld3d::create()
|
|||||||
for (j = -sy; j <= sy; j++)
|
for (j = -sy; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++)
|
for (i = -sx; i <= sx; i++)
|
||||||
if (k > 0 || j > 0 || (j == 0 && i > 0)) {
|
if (k > 0 || j > 0 || (j == 0 && i > 0)) {
|
||||||
rsq = bin_distance(i,j,k);
|
rsq = bin_distance(i, j, k);
|
||||||
if (rsq < typesq) {
|
if (rsq < typesq) {
|
||||||
distsq[n] = rsq;
|
distsq[n] = rsq;
|
||||||
s[n++] = k*mbiny*mbinx + j*mbinx + i;
|
s[n++] = k * mbiny * mbinx + j * mbinx + i;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
nstencil_multi_old[itype] = n;
|
nstencil_multi_old[itype] = n;
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -19,8 +18,7 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
NStencilHalfMultiOld3dTri::
|
NStencilHalfMultiOld3dTri::NStencilHalfMultiOld3dTri(LAMMPS *lmp) : NStencil(lmp) {}
|
||||||
NStencilHalfMultiOld3dTri(LAMMPS *lmp) : NStencil(lmp) {}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
create stencil based on bin geometry and cutoff
|
create stencil based on bin geometry and cutoff
|
||||||
@ -28,8 +26,8 @@ NStencilHalfMultiOld3dTri(LAMMPS *lmp) : NStencil(lmp) {}
|
|||||||
|
|
||||||
void NStencilHalfMultiOld3dTri::create()
|
void NStencilHalfMultiOld3dTri::create()
|
||||||
{
|
{
|
||||||
int i,j,k,n;
|
int i, j, k, n;
|
||||||
double rsq,typesq;
|
double rsq, typesq;
|
||||||
int *s;
|
int *s;
|
||||||
double *distsq;
|
double *distsq;
|
||||||
|
|
||||||
@ -42,10 +40,10 @@ void NStencilHalfMultiOld3dTri::create()
|
|||||||
for (k = 0; k <= sz; k++)
|
for (k = 0; k <= sz; k++)
|
||||||
for (j = -sy; j <= sy; j++)
|
for (j = -sy; j <= sy; j++)
|
||||||
for (i = -sx; i <= sx; i++) {
|
for (i = -sx; i <= sx; i++) {
|
||||||
rsq = bin_distance(i,j,k);
|
rsq = bin_distance(i, j, k);
|
||||||
if (rsq < typesq) {
|
if (rsq < typesq) {
|
||||||
distsq[n] = rsq;
|
distsq[n] = rsq;
|
||||||
s[n++] = k*mbiny*mbinx + j*mbinx + i;
|
s[n++] = k * mbiny * mbinx + j * mbinx + i;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
nstencil_multi_old[itype] = n;
|
nstencil_multi_old[itype] = n;
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -15,14 +14,13 @@
|
|||||||
#include "ntopo_bond_all.h"
|
#include "ntopo_bond_all.h"
|
||||||
|
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "force.h"
|
|
||||||
#include "domain.h"
|
#include "domain.h"
|
||||||
#include "update.h"
|
#include "error.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "memory.h"
|
||||||
#include "output.h"
|
#include "output.h"
|
||||||
#include "thermo.h"
|
#include "thermo.h"
|
||||||
#include "memory.h"
|
#include "update.h"
|
||||||
#include "error.h"
|
|
||||||
|
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -39,7 +37,7 @@ NTopoBondAll::NTopoBondAll(LAMMPS *lmp) : NTopo(lmp)
|
|||||||
|
|
||||||
void NTopoBondAll::build()
|
void NTopoBondAll::build()
|
||||||
{
|
{
|
||||||
int i,m,atom1;
|
int i, m, atom1;
|
||||||
|
|
||||||
int nlocal = atom->nlocal;
|
int nlocal = atom->nlocal;
|
||||||
int *num_bond = atom->num_bond;
|
int *num_bond = atom->num_bond;
|
||||||
@ -58,16 +56,17 @@ void NTopoBondAll::build()
|
|||||||
if (atom1 == -1) {
|
if (atom1 == -1) {
|
||||||
nmissing++;
|
nmissing++;
|
||||||
if (lostbond == Thermo::ERROR)
|
if (lostbond == Thermo::ERROR)
|
||||||
error->one(FLERR,"Bond atoms {} {} missing on "
|
error->one(FLERR,
|
||||||
"proc {} at step {}",tag[i],
|
"Bond atoms {} {} missing on "
|
||||||
bond_atom[i][m],me,update->ntimestep);
|
"proc {} at step {}",
|
||||||
|
tag[i], bond_atom[i][m], me, update->ntimestep);
|
||||||
continue;
|
continue;
|
||||||
}
|
}
|
||||||
atom1 = domain->closest_image(i,atom1);
|
atom1 = domain->closest_image(i, atom1);
|
||||||
if (newton_bond || i < atom1) {
|
if (newton_bond || i < atom1) {
|
||||||
if (nbondlist == maxbond) {
|
if (nbondlist == maxbond) {
|
||||||
maxbond += DELTA;
|
maxbond += DELTA;
|
||||||
memory->grow(bondlist,maxbond,3,"neigh_topo:bondlist");
|
memory->grow(bondlist, maxbond, 3, "neigh_topo:bondlist");
|
||||||
}
|
}
|
||||||
bondlist[nbondlist][0] = i;
|
bondlist[nbondlist][0] = i;
|
||||||
bondlist[nbondlist][1] = atom1;
|
bondlist[nbondlist][1] = atom1;
|
||||||
@ -80,7 +79,6 @@ void NTopoBondAll::build()
|
|||||||
if (lostbond == Thermo::IGNORE) return;
|
if (lostbond == Thermo::IGNORE) return;
|
||||||
|
|
||||||
int all;
|
int all;
|
||||||
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
|
MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world);
|
||||||
if (all && (me == 0))
|
if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}", update->ntimestep);
|
||||||
error->warning(FLERR,"Bond atoms missing at step {}",update->ntimestep);
|
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -15,14 +14,13 @@
|
|||||||
#include "ntopo_bond_partial.h"
|
#include "ntopo_bond_partial.h"
|
||||||
|
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "force.h"
|
|
||||||
#include "domain.h"
|
#include "domain.h"
|
||||||
#include "update.h"
|
#include "error.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "memory.h"
|
||||||
#include "output.h"
|
#include "output.h"
|
||||||
#include "thermo.h"
|
#include "thermo.h"
|
||||||
#include "memory.h"
|
#include "update.h"
|
||||||
#include "error.h"
|
|
||||||
|
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -39,7 +37,7 @@ NTopoBondPartial::NTopoBondPartial(LAMMPS *lmp) : NTopo(lmp)
|
|||||||
|
|
||||||
void NTopoBondPartial::build()
|
void NTopoBondPartial::build()
|
||||||
{
|
{
|
||||||
int i,m,atom1;
|
int i, m, atom1;
|
||||||
|
|
||||||
int nlocal = atom->nlocal;
|
int nlocal = atom->nlocal;
|
||||||
int *num_bond = atom->num_bond;
|
int *num_bond = atom->num_bond;
|
||||||
@ -59,16 +57,17 @@ void NTopoBondPartial::build()
|
|||||||
if (atom1 == -1) {
|
if (atom1 == -1) {
|
||||||
nmissing++;
|
nmissing++;
|
||||||
if (lostbond == Thermo::ERROR)
|
if (lostbond == Thermo::ERROR)
|
||||||
error->one(FLERR,"Bond atoms {} {} missing on "
|
error->one(FLERR,
|
||||||
"proc {} at step {}",tag[i],
|
"Bond atoms {} {} missing on "
|
||||||
bond_atom[i][m],me,update->ntimestep);
|
"proc {} at step {}",
|
||||||
|
tag[i], bond_atom[i][m], me, update->ntimestep);
|
||||||
continue;
|
continue;
|
||||||
}
|
}
|
||||||
atom1 = domain->closest_image(i,atom1);
|
atom1 = domain->closest_image(i, atom1);
|
||||||
if (newton_bond || i < atom1) {
|
if (newton_bond || i < atom1) {
|
||||||
if (nbondlist == maxbond) {
|
if (nbondlist == maxbond) {
|
||||||
maxbond += DELTA;
|
maxbond += DELTA;
|
||||||
memory->grow(bondlist,maxbond,3,"neigh_topo:bondlist");
|
memory->grow(bondlist, maxbond, 3, "neigh_topo:bondlist");
|
||||||
}
|
}
|
||||||
bondlist[nbondlist][0] = i;
|
bondlist[nbondlist][0] = i;
|
||||||
bondlist[nbondlist][1] = atom1;
|
bondlist[nbondlist][1] = atom1;
|
||||||
@ -81,7 +80,6 @@ void NTopoBondPartial::build()
|
|||||||
if (lostbond == Thermo::IGNORE) return;
|
if (lostbond == Thermo::IGNORE) return;
|
||||||
|
|
||||||
int all;
|
int all;
|
||||||
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
|
MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world);
|
||||||
if (all && (me == 0))
|
if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}", update->ntimestep);
|
||||||
error->warning(FLERR,"Bond atoms missing at step {}",update->ntimestep);
|
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -18,11 +17,10 @@
|
|||||||
|
|
||||||
#include "pair_deprecated.h"
|
#include "pair_deprecated.h"
|
||||||
|
|
||||||
#include "pair_hybrid.h"
|
|
||||||
#include "comm.h"
|
#include "comm.h"
|
||||||
#include "force.h"
|
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "pair_hybrid.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -35,21 +33,21 @@ void PairDeprecated::settings(int, char **)
|
|||||||
// hybrid substyles are created in PairHybrid::settings(), so when this is
|
// hybrid substyles are created in PairHybrid::settings(), so when this is
|
||||||
// called, our style was just added at the end of the list of substyles
|
// called, our style was just added at the end of the list of substyles
|
||||||
|
|
||||||
if (utils::strmatch(my_style,"^hybrid")) {
|
if (utils::strmatch(my_style, "^hybrid")) {
|
||||||
auto hybrid = dynamic_cast<PairHybrid *>(force->pair);
|
auto hybrid = dynamic_cast<PairHybrid *>(force->pair);
|
||||||
my_style = hybrid->keywords[hybrid->nstyles];
|
my_style = hybrid->keywords[hybrid->nstyles];
|
||||||
}
|
}
|
||||||
|
|
||||||
if (my_style == "DEPRECATED") {
|
if (my_style == "DEPRECATED") {
|
||||||
if (lmp->comm->me == 0)
|
if (lmp->comm->me == 0) utils::logmesg(lmp, "\nPair style 'DEPRECATED' is a dummy style\n\n");
|
||||||
utils::logmesg(lmp,"\nPair style 'DEPRECATED' is a dummy style\n\n");
|
|
||||||
return;
|
return;
|
||||||
}
|
}
|
||||||
|
|
||||||
if (my_style == "reax") {
|
if (my_style == "reax") {
|
||||||
if (lmp->comm->me == 0)
|
if (lmp->comm->me == 0)
|
||||||
utils::logmesg(lmp,"\nPair style 'reax' has been removed from LAMMPS "
|
utils::logmesg(lmp,
|
||||||
|
"\nPair style 'reax' has been removed from LAMMPS "
|
||||||
"after the 12 December 2018 version\n\n");
|
"after the 12 December 2018 version\n\n");
|
||||||
}
|
}
|
||||||
error->all(FLERR,"This pair style is no longer available");
|
error->all(FLERR, "This pair style is no longer available");
|
||||||
}
|
}
|
||||||
|
|||||||
@ -395,20 +395,18 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
|
|||||||
union_int_float_t rsq_lookup;
|
union_int_float_t rsq_lookup;
|
||||||
|
|
||||||
int rerror = 0;
|
int rerror = 0;
|
||||||
int cerror = 0;
|
|
||||||
|
|
||||||
reader.skip_line();
|
reader.skip_line();
|
||||||
for (int i = 0; i < tb->ninput; i++) {
|
for (int i = 0; i < tb->ninput; i++) {
|
||||||
line = reader.next_line(4);
|
line = reader.next_line();
|
||||||
|
|
||||||
try {
|
try {
|
||||||
ValueTokenizer values(line);
|
ValueTokenizer values(line);
|
||||||
values.next_int();
|
values.next_int();
|
||||||
rfile = values.next_double();
|
rfile = values.next_double();
|
||||||
tb->efile[i] = conversion_factor * values.next_double();
|
tb->efile[i] = conversion_factor * values.next_double();
|
||||||
tb->ffile[i] = conversion_factor * values.next_double();
|
tb->ffile[i] = conversion_factor * values.next_double();
|
||||||
} catch (TokenizerException &) {
|
} catch (TokenizerException &e) {
|
||||||
++cerror;
|
error->one(FLERR, "Error parsing pair table '{}' line {} of {}. {}\nLine was: {}", keyword,
|
||||||
|
i + 1, tb->ninput, e.what(), line);
|
||||||
}
|
}
|
||||||
|
|
||||||
rnew = rfile;
|
rnew = rfile;
|
||||||
@ -474,14 +472,6 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
|
|||||||
"{} of {} distance values in table {} with relative error\n"
|
"{} of {} distance values in table {} with relative error\n"
|
||||||
"WARNING: over {} to re-computed values",
|
"WARNING: over {} to re-computed values",
|
||||||
rerror, tb->ninput, EPSILONR, keyword);
|
rerror, tb->ninput, EPSILONR, keyword);
|
||||||
|
|
||||||
// warn if data was read incompletely, e.g. columns were missing
|
|
||||||
|
|
||||||
if (cerror)
|
|
||||||
error->warning(FLERR,
|
|
||||||
"{} of {} lines in table {} were incomplete\n"
|
|
||||||
"WARNING: or could not be parsed completely",
|
|
||||||
cerror, tb->ninput, keyword);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -14,14 +13,14 @@
|
|||||||
|
|
||||||
#include "pair_yukawa.h"
|
#include "pair_yukawa.h"
|
||||||
|
|
||||||
#include <cmath>
|
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "force.h"
|
|
||||||
#include "comm.h"
|
#include "comm.h"
|
||||||
#include "neigh_list.h"
|
|
||||||
#include "memory.h"
|
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
|
||||||
|
#include <cmath>
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -53,13 +52,13 @@ PairYukawa::~PairYukawa()
|
|||||||
|
|
||||||
void PairYukawa::compute(int eflag, int vflag)
|
void PairYukawa::compute(int eflag, int vflag)
|
||||||
{
|
{
|
||||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
int i, j, ii, jj, inum, jnum, itype, jtype;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
|
||||||
double rsq,r2inv,r,rinv,screening,forceyukawa,factor;
|
double rsq, r2inv, r, rinv, screening, forceyukawa, factor;
|
||||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||||
|
|
||||||
evdwl = 0.0;
|
evdwl = 0.0;
|
||||||
ev_init(eflag,vflag);
|
ev_init(eflag, vflag);
|
||||||
|
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
double **f = atom->f;
|
double **f = atom->f;
|
||||||
@ -92,25 +91,25 @@ void PairYukawa::compute(int eflag, int vflag)
|
|||||||
delx = xtmp - x[j][0];
|
delx = xtmp - x[j][0];
|
||||||
dely = ytmp - x[j][1];
|
dely = ytmp - x[j][1];
|
||||||
delz = ztmp - x[j][2];
|
delz = ztmp - x[j][2];
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
rsq = delx * delx + dely * dely + delz * delz;
|
||||||
jtype = type[j];
|
jtype = type[j];
|
||||||
|
|
||||||
if (rsq < cutsq[itype][jtype]) {
|
if (rsq < cutsq[itype][jtype]) {
|
||||||
r2inv = 1.0/rsq;
|
r2inv = 1.0 / rsq;
|
||||||
r = sqrt(rsq);
|
r = sqrt(rsq);
|
||||||
rinv = 1.0/r;
|
rinv = 1.0 / r;
|
||||||
screening = exp(-kappa*r);
|
screening = exp(-kappa * r);
|
||||||
forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
|
forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
|
||||||
|
|
||||||
fpair = factor*forceyukawa * r2inv;
|
fpair = factor * forceyukawa * r2inv;
|
||||||
|
|
||||||
f[i][0] += delx*fpair;
|
f[i][0] += delx * fpair;
|
||||||
f[i][1] += dely*fpair;
|
f[i][1] += dely * fpair;
|
||||||
f[i][2] += delz*fpair;
|
f[i][2] += delz * fpair;
|
||||||
if (newton_pair || j < nlocal) {
|
if (newton_pair || j < nlocal) {
|
||||||
f[j][0] -= delx*fpair;
|
f[j][0] -= delx * fpair;
|
||||||
f[j][1] -= dely*fpair;
|
f[j][1] -= dely * fpair;
|
||||||
f[j][2] -= delz*fpair;
|
f[j][2] -= delz * fpair;
|
||||||
}
|
}
|
||||||
|
|
||||||
if (eflag) {
|
if (eflag) {
|
||||||
@ -118,8 +117,7 @@ void PairYukawa::compute(int eflag, int vflag)
|
|||||||
evdwl *= factor;
|
evdwl *= factor;
|
||||||
}
|
}
|
||||||
|
|
||||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
|
||||||
evdwl,0.0,fpair,delx,dely,delz);
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -134,18 +132,17 @@ void PairYukawa::compute(int eflag, int vflag)
|
|||||||
void PairYukawa::allocate()
|
void PairYukawa::allocate()
|
||||||
{
|
{
|
||||||
allocated = 1;
|
allocated = 1;
|
||||||
int n = atom->ntypes;
|
int np1 = atom->ntypes + 1;
|
||||||
|
|
||||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
memory->create(setflag, np1, np1, "pair:setflag");
|
||||||
for (int i = 1; i <= n; i++)
|
for (int i = 1; i < np1; i++)
|
||||||
for (int j = i; j <= n; j++)
|
for (int j = i; j < np1; j++) setflag[i][j] = 0;
|
||||||
setflag[i][j] = 0;
|
|
||||||
|
|
||||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
memory->create(cutsq, np1, np1, "pair:cutsq");
|
||||||
memory->create(rad,n+1,"pair:rad");
|
memory->create(rad, np1, "pair:rad");
|
||||||
memory->create(cut,n+1,n+1,"pair:cut");
|
memory->create(cut, np1, np1, "pair:cut");
|
||||||
memory->create(a,n+1,n+1,"pair:a");
|
memory->create(a, np1, np1, "pair:a");
|
||||||
memory->create(offset,n+1,n+1,"pair:offset");
|
memory->create(offset, np1, np1, "pair:offset");
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -154,15 +151,15 @@ void PairYukawa::allocate()
|
|||||||
|
|
||||||
void PairYukawa::settings(int narg, char **arg)
|
void PairYukawa::settings(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
|
if (narg != 2) error->all(FLERR, "Illegal pair_style command");
|
||||||
|
|
||||||
kappa = utils::numeric(FLERR,arg[0],false,lmp);
|
kappa = utils::numeric(FLERR, arg[0], false, lmp);
|
||||||
cut_global = utils::numeric(FLERR,arg[1],false,lmp);
|
cut_global = utils::numeric(FLERR, arg[1], false, lmp);
|
||||||
|
|
||||||
// reset cutoffs that have been explicitly set
|
// reset cutoffs that have been explicitly set
|
||||||
|
|
||||||
if (allocated) {
|
if (allocated) {
|
||||||
int i,j;
|
int i, j;
|
||||||
for (i = 1; i <= atom->ntypes; i++)
|
for (i = 1; i <= atom->ntypes; i++)
|
||||||
for (j = i; j <= atom->ntypes; j++)
|
for (j = i; j <= atom->ntypes; j++)
|
||||||
if (setflag[i][j]) cut[i][j] = cut_global;
|
if (setflag[i][j]) cut[i][j] = cut_global;
|
||||||
@ -175,22 +172,21 @@ void PairYukawa::settings(int narg, char **arg)
|
|||||||
|
|
||||||
void PairYukawa::coeff(int narg, char **arg)
|
void PairYukawa::coeff(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (narg < 3 || narg > 4)
|
if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect args for pair coefficients");
|
||||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
|
||||||
if (!allocated) allocate();
|
if (!allocated) allocate();
|
||||||
|
|
||||||
int ilo,ihi,jlo,jhi;
|
int ilo, ihi, jlo, jhi;
|
||||||
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
|
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
|
||||||
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
|
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
|
||||||
|
|
||||||
double a_one = utils::numeric(FLERR,arg[2],false,lmp);
|
double a_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||||
|
|
||||||
double cut_one = cut_global;
|
double cut_one = cut_global;
|
||||||
if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],false,lmp);
|
if (narg == 4) cut_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||||
|
|
||||||
int count = 0;
|
int count = 0;
|
||||||
for (int i = ilo; i <= ihi; i++) {
|
for (int i = ilo; i <= ihi; i++) {
|
||||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
for (int j = MAX(jlo, i); j <= jhi; j++) {
|
||||||
a[i][j] = a_one;
|
a[i][j] = a_one;
|
||||||
cut[i][j] = cut_one;
|
cut[i][j] = cut_one;
|
||||||
setflag[i][j] = 1;
|
setflag[i][j] = 1;
|
||||||
@ -198,7 +194,7 @@ void PairYukawa::coeff(int narg, char **arg)
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -208,14 +204,15 @@ void PairYukawa::coeff(int narg, char **arg)
|
|||||||
double PairYukawa::init_one(int i, int j)
|
double PairYukawa::init_one(int i, int j)
|
||||||
{
|
{
|
||||||
if (setflag[i][j] == 0) {
|
if (setflag[i][j] == 0) {
|
||||||
a[i][j] = mix_energy(a[i][i],a[j][j],1.0,1.0);
|
a[i][j] = mix_energy(a[i][i], a[j][j], 1.0, 1.0);
|
||||||
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
|
cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
|
||||||
}
|
}
|
||||||
|
|
||||||
if (offset_flag && (cut[i][j] > 0.0)) {
|
if (offset_flag && (cut[i][j] > 0.0)) {
|
||||||
double screening = exp(-kappa * cut[i][j]);
|
double screening = exp(-kappa * cut[i][j]);
|
||||||
offset[i][j] = a[i][j] * screening / cut[i][j];
|
offset[i][j] = a[i][j] * screening / cut[i][j];
|
||||||
} else offset[i][j] = 0.0;
|
} else
|
||||||
|
offset[i][j] = 0.0;
|
||||||
|
|
||||||
a[j][i] = a[i][j];
|
a[j][i] = a[i][j];
|
||||||
offset[j][i] = offset[i][j];
|
offset[j][i] = offset[i][j];
|
||||||
@ -231,13 +228,13 @@ void PairYukawa::write_restart(FILE *fp)
|
|||||||
{
|
{
|
||||||
write_restart_settings(fp);
|
write_restart_settings(fp);
|
||||||
|
|
||||||
int i,j;
|
int i, j;
|
||||||
for (i = 1; i <= atom->ntypes; i++)
|
for (i = 1; i <= atom->ntypes; i++)
|
||||||
for (j = i; j <= atom->ntypes; j++) {
|
for (j = i; j <= atom->ntypes; j++) {
|
||||||
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
fwrite(&setflag[i][j], sizeof(int), 1, fp);
|
||||||
if (setflag[i][j]) {
|
if (setflag[i][j]) {
|
||||||
fwrite(&a[i][j],sizeof(double),1,fp);
|
fwrite(&a[i][j], sizeof(double), 1, fp);
|
||||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
fwrite(&cut[i][j], sizeof(double), 1, fp);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -252,19 +249,19 @@ void PairYukawa::read_restart(FILE *fp)
|
|||||||
|
|
||||||
allocate();
|
allocate();
|
||||||
|
|
||||||
int i,j;
|
int i, j;
|
||||||
int me = comm->me;
|
int me = comm->me;
|
||||||
for (i = 1; i <= atom->ntypes; i++)
|
for (i = 1; i <= atom->ntypes; i++)
|
||||||
for (j = i; j <= atom->ntypes; j++) {
|
for (j = i; j <= atom->ntypes; j++) {
|
||||||
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
|
if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
|
||||||
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
|
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
|
||||||
if (setflag[i][j]) {
|
if (setflag[i][j]) {
|
||||||
if (me == 0) {
|
if (me == 0) {
|
||||||
utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,nullptr,error);
|
utils::sfread(FLERR, &a[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||||
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
|
utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
|
||||||
}
|
}
|
||||||
MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
|
MPI_Bcast(&a[i][j], 1, MPI_DOUBLE, 0, world);
|
||||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -275,10 +272,10 @@ void PairYukawa::read_restart(FILE *fp)
|
|||||||
|
|
||||||
void PairYukawa::write_restart_settings(FILE *fp)
|
void PairYukawa::write_restart_settings(FILE *fp)
|
||||||
{
|
{
|
||||||
fwrite(&kappa,sizeof(double),1,fp);
|
fwrite(&kappa, sizeof(double), 1, fp);
|
||||||
fwrite(&cut_global,sizeof(double),1,fp);
|
fwrite(&cut_global, sizeof(double), 1, fp);
|
||||||
fwrite(&offset_flag,sizeof(int),1,fp);
|
fwrite(&offset_flag, sizeof(int), 1, fp);
|
||||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
fwrite(&mix_flag, sizeof(int), 1, fp);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -288,15 +285,15 @@ void PairYukawa::write_restart_settings(FILE *fp)
|
|||||||
void PairYukawa::read_restart_settings(FILE *fp)
|
void PairYukawa::read_restart_settings(FILE *fp)
|
||||||
{
|
{
|
||||||
if (comm->me == 0) {
|
if (comm->me == 0) {
|
||||||
utils::sfread(FLERR,&kappa,sizeof(double),1,fp,nullptr,error);
|
utils::sfread(FLERR, &kappa, sizeof(double), 1, fp, nullptr, error);
|
||||||
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
|
utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error);
|
||||||
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error);
|
utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error);
|
||||||
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
|
utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error);
|
||||||
}
|
}
|
||||||
MPI_Bcast(&kappa,1,MPI_DOUBLE,0,world);
|
MPI_Bcast(&kappa, 1, MPI_DOUBLE, 0, world);
|
||||||
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world);
|
||||||
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world);
|
||||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -305,8 +302,7 @@ void PairYukawa::read_restart_settings(FILE *fp)
|
|||||||
|
|
||||||
void PairYukawa::write_data(FILE *fp)
|
void PairYukawa::write_data(FILE *fp)
|
||||||
{
|
{
|
||||||
for (int i = 1; i <= atom->ntypes; i++)
|
for (int i = 1; i <= atom->ntypes; i++) fprintf(fp, "%d %g\n", i, a[i][i]);
|
||||||
fprintf(fp,"%d %g\n",i,a[i][i]);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -316,25 +312,23 @@ void PairYukawa::write_data(FILE *fp)
|
|||||||
void PairYukawa::write_data_all(FILE *fp)
|
void PairYukawa::write_data_all(FILE *fp)
|
||||||
{
|
{
|
||||||
for (int i = 1; i <= atom->ntypes; i++)
|
for (int i = 1; i <= atom->ntypes; i++)
|
||||||
for (int j = i; j <= atom->ntypes; j++)
|
for (int j = i; j <= atom->ntypes; j++) fprintf(fp, "%d %d %g %g\n", i, j, a[i][j], cut[i][j]);
|
||||||
fprintf(fp,"%d %d %g %g\n",i,j,a[i][j],cut[i][j]);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
double PairYukawa::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
|
double PairYukawa::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
|
||||||
double /*factor_coul*/, double factor_lj,
|
double /*factor_coul*/, double factor_lj, double &fforce)
|
||||||
double &fforce)
|
|
||||||
{
|
{
|
||||||
double r2inv,r,rinv,screening,forceyukawa,phi;
|
double r2inv, r, rinv, screening, forceyukawa, phi;
|
||||||
|
|
||||||
r2inv = 1.0/rsq;
|
r2inv = 1.0 / rsq;
|
||||||
r = sqrt(rsq);
|
r = sqrt(rsq);
|
||||||
rinv = 1.0/r;
|
rinv = 1.0 / r;
|
||||||
screening = exp(-kappa*r);
|
screening = exp(-kappa * r);
|
||||||
forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
|
forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
|
||||||
fforce = factor_lj*forceyukawa * r2inv;
|
fforce = factor_lj * forceyukawa * r2inv;
|
||||||
|
|
||||||
phi = a[itype][jtype] * screening * rinv - offset[itype][jtype];
|
phi = a[itype][jtype] * screening * rinv - offset[itype][jtype];
|
||||||
return factor_lj*phi;
|
return factor_lj * phi;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -20,8 +19,8 @@
|
|||||||
|
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "comm.h"
|
#include "comm.h"
|
||||||
#include "memory.h"
|
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
#include "memory.h"
|
||||||
|
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
|
|
||||||
@ -29,11 +28,12 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
PairZero::PairZero(LAMMPS *lmp) : Pair(lmp) {
|
PairZero::PairZero(LAMMPS *lmp) : Pair(lmp)
|
||||||
coeffflag=1;
|
{
|
||||||
writedata=1;
|
coeffflag = 1;
|
||||||
single_enable=1;
|
writedata = 1;
|
||||||
respa_enable=1;
|
single_enable = 1;
|
||||||
|
respa_enable = 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -51,15 +51,15 @@ PairZero::~PairZero()
|
|||||||
|
|
||||||
void PairZero::compute(int eflag, int vflag)
|
void PairZero::compute(int eflag, int vflag)
|
||||||
{
|
{
|
||||||
ev_init(eflag,vflag);
|
ev_init(eflag, vflag);
|
||||||
if (vflag_fdotr) virial_fdotr_compute();
|
if (vflag_fdotr) virial_fdotr_compute();
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void PairZero::compute_outer(int eflag, int vflag)
|
void PairZero::compute_outer(int eflag, int vflag)
|
||||||
{
|
{
|
||||||
ev_init(eflag,vflag);
|
ev_init(eflag, vflag);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -69,15 +69,14 @@ void PairZero::compute_outer(int eflag, int vflag)
|
|||||||
void PairZero::allocate()
|
void PairZero::allocate()
|
||||||
{
|
{
|
||||||
allocated = 1;
|
allocated = 1;
|
||||||
int n = atom->ntypes;
|
int np1 = atom->ntypes + 1;
|
||||||
|
|
||||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
memory->create(setflag, np1, np1, "pair:setflag");
|
||||||
for (int i = 1; i <= n; i++)
|
for (int i = 1; i < np1; i++)
|
||||||
for (int j = i; j <= n; j++)
|
for (int j = i; j < np1; j++) setflag[i][j] = 0;
|
||||||
setflag[i][j] = 0;
|
|
||||||
|
|
||||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
memory->create(cutsq, np1, np1, "pair:cutsq");
|
||||||
memory->create(cut,n+1,n+1,"pair:cut");
|
memory->create(cut, np1, np1, "pair:cut");
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -86,22 +85,22 @@ void PairZero::allocate()
|
|||||||
|
|
||||||
void PairZero::settings(int narg, char **arg)
|
void PairZero::settings(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if ((narg != 1) && (narg != 2))
|
if ((narg != 1) && (narg != 2)) error->all(FLERR, "Illegal pair_style command");
|
||||||
error->all(FLERR,"Illegal pair_style command");
|
|
||||||
|
|
||||||
cut_global = utils::numeric(FLERR,arg[0],false,lmp);
|
cut_global = utils::numeric(FLERR, arg[0], false, lmp);
|
||||||
if (narg == 2) {
|
if (narg == 2) {
|
||||||
if (strcmp("nocoeff",arg[1]) == 0) coeffflag=0;
|
if (strcmp("nocoeff", arg[1]) == 0)
|
||||||
else error->all(FLERR,"Illegal pair_style command");
|
coeffflag = 0;
|
||||||
|
else
|
||||||
|
error->all(FLERR, "Illegal pair_style command");
|
||||||
}
|
}
|
||||||
|
|
||||||
// reset cutoffs that have been explicitly set
|
// reset cutoffs that have been explicitly set
|
||||||
|
|
||||||
if (allocated) {
|
if (allocated) {
|
||||||
int i,j;
|
int i, j;
|
||||||
for (i = 1; i <= atom->ntypes; i++)
|
for (i = 1; i <= atom->ntypes; i++)
|
||||||
for (j = i+1; j <= atom->ntypes; j++)
|
for (j = i + 1; j <= atom->ntypes; j++) cut[i][j] = cut_global;
|
||||||
cut[i][j] = cut_global;
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -112,27 +111,27 @@ void PairZero::settings(int narg, char **arg)
|
|||||||
void PairZero::coeff(int narg, char **arg)
|
void PairZero::coeff(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if ((narg < 2) || (coeffflag && narg > 3))
|
if ((narg < 2) || (coeffflag && narg > 3))
|
||||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
error->all(FLERR, "Incorrect args for pair coefficients");
|
||||||
|
|
||||||
if (!allocated) allocate();
|
if (!allocated) allocate();
|
||||||
|
|
||||||
int ilo,ihi,jlo,jhi;
|
int ilo, ihi, jlo, jhi;
|
||||||
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
|
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
|
||||||
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
|
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
|
||||||
|
|
||||||
double cut_one = cut_global;
|
double cut_one = cut_global;
|
||||||
if (coeffflag && (narg == 3)) cut_one = utils::numeric(FLERR,arg[2],false,lmp);
|
if (coeffflag && (narg == 3)) cut_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||||
|
|
||||||
int count = 0;
|
int count = 0;
|
||||||
for (int i = ilo; i <= ihi; i++) {
|
for (int i = ilo; i <= ihi; i++) {
|
||||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
for (int j = MAX(jlo, i); j <= jhi; j++) {
|
||||||
cut[i][j] = cut_one;
|
cut[i][j] = cut_one;
|
||||||
setflag[i][j] = 1;
|
setflag[i][j] = 1;
|
||||||
count++;
|
count++;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -141,9 +140,7 @@ void PairZero::coeff(int narg, char **arg)
|
|||||||
|
|
||||||
double PairZero::init_one(int i, int j)
|
double PairZero::init_one(int i, int j)
|
||||||
{
|
{
|
||||||
if (setflag[i][j] == 0) {
|
if (setflag[i][j] == 0) { cut[i][j] = mix_distance(cut[i][i], cut[j][j]); }
|
||||||
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
|
|
||||||
}
|
|
||||||
|
|
||||||
return cut[i][j];
|
return cut[i][j];
|
||||||
}
|
}
|
||||||
@ -156,13 +153,11 @@ void PairZero::write_restart(FILE *fp)
|
|||||||
{
|
{
|
||||||
write_restart_settings(fp);
|
write_restart_settings(fp);
|
||||||
|
|
||||||
int i,j;
|
int i, j;
|
||||||
for (i = 1; i <= atom->ntypes; i++)
|
for (i = 1; i <= atom->ntypes; i++)
|
||||||
for (j = i; j <= atom->ntypes; j++) {
|
for (j = i; j <= atom->ntypes; j++) {
|
||||||
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
fwrite(&setflag[i][j], sizeof(int), 1, fp);
|
||||||
if (setflag[i][j]) {
|
if (setflag[i][j]) { fwrite(&cut[i][j], sizeof(double), 1, fp); }
|
||||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -175,17 +170,15 @@ void PairZero::read_restart(FILE *fp)
|
|||||||
read_restart_settings(fp);
|
read_restart_settings(fp);
|
||||||
allocate();
|
allocate();
|
||||||
|
|
||||||
int i,j;
|
int i, j;
|
||||||
int me = comm->me;
|
int me = comm->me;
|
||||||
for (i = 1; i <= atom->ntypes; i++)
|
for (i = 1; i <= atom->ntypes; i++)
|
||||||
for (j = i; j <= atom->ntypes; j++) {
|
for (j = i; j <= atom->ntypes; j++) {
|
||||||
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
|
if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
|
||||||
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
|
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
|
||||||
if (setflag[i][j]) {
|
if (setflag[i][j]) {
|
||||||
if (me == 0) {
|
if (me == 0) { utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error); }
|
||||||
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
|
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
|
||||||
}
|
|
||||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -196,8 +189,8 @@ void PairZero::read_restart(FILE *fp)
|
|||||||
|
|
||||||
void PairZero::write_restart_settings(FILE *fp)
|
void PairZero::write_restart_settings(FILE *fp)
|
||||||
{
|
{
|
||||||
fwrite(&cut_global,sizeof(double),1,fp);
|
fwrite(&cut_global, sizeof(double), 1, fp);
|
||||||
fwrite(&coeffflag,sizeof(int),1,fp);
|
fwrite(&coeffflag, sizeof(int), 1, fp);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -208,11 +201,11 @@ void PairZero::read_restart_settings(FILE *fp)
|
|||||||
{
|
{
|
||||||
int me = comm->me;
|
int me = comm->me;
|
||||||
if (me == 0) {
|
if (me == 0) {
|
||||||
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
|
utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error);
|
||||||
utils::sfread(FLERR,&coeffflag,sizeof(int),1,fp,nullptr,error);
|
utils::sfread(FLERR, &coeffflag, sizeof(int), 1, fp, nullptr, error);
|
||||||
}
|
}
|
||||||
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world);
|
||||||
MPI_Bcast(&coeffflag,1,MPI_INT,0,world);
|
MPI_Bcast(&coeffflag, 1, MPI_INT, 0, world);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -221,8 +214,7 @@ void PairZero::read_restart_settings(FILE *fp)
|
|||||||
|
|
||||||
void PairZero::write_data(FILE *fp)
|
void PairZero::write_data(FILE *fp)
|
||||||
{
|
{
|
||||||
for (int i = 1; i <= atom->ntypes; i++)
|
for (int i = 1; i <= atom->ntypes; i++) fprintf(fp, "%d\n", i);
|
||||||
fprintf(fp,"%d\n",i);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -232,17 +224,14 @@ void PairZero::write_data(FILE *fp)
|
|||||||
void PairZero::write_data_all(FILE *fp)
|
void PairZero::write_data_all(FILE *fp)
|
||||||
{
|
{
|
||||||
for (int i = 1; i <= atom->ntypes; i++)
|
for (int i = 1; i <= atom->ntypes; i++)
|
||||||
for (int j = i; j <= atom->ntypes; j++)
|
for (int j = i; j <= atom->ntypes; j++) fprintf(fp, "%d %d %g\n", i, j, cut[i][j]);
|
||||||
fprintf(fp,"%d %d %g\n",i,j,cut[i][j]);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
double PairZero::single(int /*i*/, int /*j*/, int /* itype */, int /* jtype */,
|
double PairZero::single(int /*i*/, int /*j*/, int /* itype */, int /* jtype */, double /* rsq */,
|
||||||
double /* rsq */, double /*factor_coul*/,
|
double /*factor_coul*/, double /* factor_lj */, double &fforce)
|
||||||
double /* factor_lj */, double &fforce)
|
|
||||||
{
|
{
|
||||||
fforce = 0.0;
|
fforce = 0.0;
|
||||||
return 0.0;
|
return 0.0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -186,13 +186,63 @@ std::string platform::os_info()
|
|||||||
char value[1024];
|
char value[1024];
|
||||||
DWORD value_length = 1024;
|
DWORD value_length = 1024;
|
||||||
const char *subkey = "SOFTWARE\\Microsoft\\Windows NT\\CurrentVersion";
|
const char *subkey = "SOFTWARE\\Microsoft\\Windows NT\\CurrentVersion";
|
||||||
const char *entry = "ProductName";
|
const char *entry = "CurrentBuild";
|
||||||
RegGetValue(HKEY_LOCAL_MACHINE, subkey, entry, RRF_RT_REG_SZ, nullptr, &value,
|
RegGetValue(HKEY_LOCAL_MACHINE, subkey, entry, RRF_RT_REG_SZ, nullptr, &value,
|
||||||
(LPDWORD) &value_length);
|
(LPDWORD) &value_length);
|
||||||
// enforce zero termination
|
// enforce zero termination
|
||||||
value[1023] = '\0';
|
value[1023] = '\0';
|
||||||
buf = value;
|
auto build = std::string(value);
|
||||||
|
|
||||||
|
if (build == "6002") {
|
||||||
|
buf = "Windows Vista";
|
||||||
|
} else if (build == "6003") {
|
||||||
|
buf = "Windows Server 2008";
|
||||||
|
} else if (build == "7601") {
|
||||||
|
buf = "Windows 7";
|
||||||
|
} else if (build == "9200") {
|
||||||
|
buf = "Windows 8";
|
||||||
|
} else if (build == "9600") {
|
||||||
|
buf = "Windows 8.1";
|
||||||
|
} else if (build == "10240") {
|
||||||
|
buf = "Windows 10 1507";
|
||||||
|
} else if (build == "10586") {
|
||||||
|
buf = "Windows 10 1511";
|
||||||
|
} else if (build == "14393") {
|
||||||
|
buf = "Windows 10 1607";
|
||||||
|
} else if (build == "15063") {
|
||||||
|
buf = "Windows 10 1703";
|
||||||
|
} else if (build == "16299") {
|
||||||
|
buf = "Windows 10 1709";
|
||||||
|
} else if (build == "17134") {
|
||||||
|
buf = "Windows 10 1803";
|
||||||
|
} else if (build == "17763") {
|
||||||
|
buf = "Windows 10 1809";
|
||||||
|
} else if (build == "18362") {
|
||||||
|
buf = "Windows 10 1903";
|
||||||
|
} else if (build == "18363") {
|
||||||
|
buf = "Windows 10 1909";
|
||||||
|
} else if (build == "19041") {
|
||||||
|
buf = "Windows 10 2004";
|
||||||
|
} else if (build == "19042") {
|
||||||
|
buf = "Windows 10 20H2";
|
||||||
|
} else if (build == "19043") {
|
||||||
|
buf = "Windows 10 21H1";
|
||||||
|
} else if (build == "19044") {
|
||||||
|
buf = "Windows 10 21H2";
|
||||||
|
} else if (build == "20348") {
|
||||||
|
buf = "Windows Server 2022";
|
||||||
|
} else if (build == "22000") {
|
||||||
|
buf = "Windows 11 21H2";
|
||||||
|
} else if (build == "22621") {
|
||||||
|
buf = "Windows 11 22H2";
|
||||||
|
} else {
|
||||||
|
const char *entry = "ProductName";
|
||||||
|
RegGetValue(HKEY_LOCAL_MACHINE, subkey, entry, RRF_RT_REG_SZ, nullptr, &value,
|
||||||
|
(LPDWORD) &value_length);
|
||||||
|
// enforce zero termination
|
||||||
|
value[1023] = '\0';
|
||||||
|
buf = value;
|
||||||
|
}
|
||||||
DWORD fullversion, majorv, minorv, buildv = 0;
|
DWORD fullversion, majorv, minorv, buildv = 0;
|
||||||
fullversion = GetVersion();
|
fullversion = GetVersion();
|
||||||
majorv = (DWORD) (LOBYTE(LOWORD(fullversion)));
|
majorv = (DWORD) (LOBYTE(LOWORD(fullversion)));
|
||||||
@ -303,11 +353,18 @@ std::string platform::compiler_info()
|
|||||||
__MINGW32_MINOR_VERSION, __VERSION__);
|
__MINGW32_MINOR_VERSION, __VERSION__);
|
||||||
#elif defined(__GNUC__)
|
#elif defined(__GNUC__)
|
||||||
buf = fmt::format("GNU C++ {}", __VERSION__);
|
buf = fmt::format("GNU C++ {}", __VERSION__);
|
||||||
#elif defined(_MSC_VER) && (_MSC_VER > 1920) && (_MSC_VER < 2000)
|
#elif defined(_MSC_VER) && (_MSC_VER >= 1920) && (_MSC_VER < 1930)
|
||||||
constexpr int major = _MSC_VER / 100;
|
constexpr int major = _MSC_VER / 100;
|
||||||
constexpr int minor = _MSC_VER - major * 100;
|
constexpr int minor = _MSC_VER - major * 100;
|
||||||
buf = "Microsoft Visual Studio 20" + std::to_string(major) + ", C/C++ " +
|
constexpr int patch = minor - 20;
|
||||||
std::to_string(major - 5) + "." + std::to_string(minor);
|
buf = fmt::format("Microsoft Visual Studio 2019 Version 16.{}, C/C++ {}.{}", patch, major - 5,
|
||||||
|
minor);
|
||||||
|
#elif defined(_MSC_VER) && (_MSC_VER >= 1930) && (_MSC_VER < 2000)
|
||||||
|
constexpr int major = _MSC_VER / 100;
|
||||||
|
constexpr int minor = _MSC_VER - major * 100;
|
||||||
|
constexpr int patch = minor - 30;
|
||||||
|
buf = fmt::format("Microsoft Visual Studio 2022 Version 17.{}, C/C++ {}.{}", patch, major - 5,
|
||||||
|
minor);
|
||||||
#else
|
#else
|
||||||
buf = "(Unknown)";
|
buf = "(Unknown)";
|
||||||
#endif
|
#endif
|
||||||
|
|||||||
@ -313,11 +313,9 @@ void ReadData::command(int narg, char **arg)
|
|||||||
error->all(FLERR,"Reading a data file with shrinkwrap boundaries is "
|
error->all(FLERR,"Reading a data file with shrinkwrap boundaries is "
|
||||||
"not compatible with a MSM KSpace style");
|
"not compatible with a MSM KSpace style");
|
||||||
if (domain->box_exist && !addflag)
|
if (domain->box_exist && !addflag)
|
||||||
error->all(FLERR,"Cannot read_data without add keyword "
|
error->all(FLERR,"Cannot read_data without add keyword after simulation box is defined");
|
||||||
"after simulation box is defined");
|
|
||||||
if (!domain->box_exist && addflag)
|
if (!domain->box_exist && addflag)
|
||||||
error->all(FLERR,"Cannot use read_data add before "
|
error->all(FLERR,"Cannot use read_data add before simulation box is defined");
|
||||||
"simulation box is defined");
|
|
||||||
if (offsetflag && addflag == NONE)
|
if (offsetflag && addflag == NONE)
|
||||||
error->all(FLERR,"Cannot use read_data offset without add flag");
|
error->all(FLERR,"Cannot use read_data offset without add flag");
|
||||||
if (shiftflag && addflag == NONE)
|
if (shiftflag && addflag == NONE)
|
||||||
@ -330,8 +328,7 @@ void ReadData::command(int narg, char **arg)
|
|||||||
// check if data file is available and readable
|
// check if data file is available and readable
|
||||||
|
|
||||||
if (!platform::file_is_readable(arg[0]))
|
if (!platform::file_is_readable(arg[0]))
|
||||||
error->all(FLERR,fmt::format("Cannot open file {}: {}",
|
error->all(FLERR,fmt::format("Cannot open file {}: {}", arg[0], utils::getsyserror()));
|
||||||
arg[0], utils::getsyserror()));
|
|
||||||
|
|
||||||
// reset so we can warn about reset image flags exactly once per data file
|
// reset so we can warn about reset image flags exactly once per data file
|
||||||
|
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -41,19 +40,19 @@ void Reader::open_file(const std::string &file)
|
|||||||
if (platform::has_compress_extension(file)) {
|
if (platform::has_compress_extension(file)) {
|
||||||
compressed = true;
|
compressed = true;
|
||||||
fp = platform::compressed_read(file);
|
fp = platform::compressed_read(file);
|
||||||
if (!fp) error->one(FLERR,"Cannot open compressed file for reading");
|
if (!fp) error->one(FLERR, "Cannot open compressed file for reading");
|
||||||
} else {
|
} else {
|
||||||
compressed = false;
|
compressed = false;
|
||||||
if (utils::strmatch(file, "\\.bin$")) {
|
if (utils::strmatch(file, "\\.bin$")) {
|
||||||
binary = true;
|
binary = true;
|
||||||
fp = fopen(file.c_str(),"rb");
|
fp = fopen(file.c_str(), "rb");
|
||||||
} else {
|
} else {
|
||||||
fp = fopen(file.c_str(),"r");
|
fp = fopen(file.c_str(), "r");
|
||||||
binary = false;
|
binary = false;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
if (!fp) error->one(FLERR,"Cannot open file {}: {}", file, utils::getsyserror());
|
if (!fp) error->one(FLERR, "Cannot open file {}: {}", file, utils::getsyserror());
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -64,8 +63,10 @@ void Reader::open_file(const std::string &file)
|
|||||||
void Reader::close_file()
|
void Reader::close_file()
|
||||||
{
|
{
|
||||||
if (fp == nullptr) return;
|
if (fp == nullptr) return;
|
||||||
if (compressed) platform::pclose(fp);
|
if (compressed)
|
||||||
else fclose(fp);
|
platform::pclose(fp);
|
||||||
|
else
|
||||||
|
fclose(fp);
|
||||||
fp = nullptr;
|
fp = nullptr;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -73,8 +74,7 @@ void Reader::close_file()
|
|||||||
detect unused arguments
|
detect unused arguments
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void Reader::settings(int narg, char** /*args*/)
|
void Reader::settings(int narg, char ** /*args*/)
|
||||||
{
|
{
|
||||||
if (narg > 0)
|
if (narg > 0) error->all(FLERR, "Illegal read_dump command");
|
||||||
error->all(FLERR,"Illegal read_dump command");
|
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -17,20 +16,17 @@
|
|||||||
#include "comm.h"
|
#include "comm.h"
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
RegionDeprecated::RegionDeprecated(LAMMPS *lmp, int narg, char **arg) :
|
RegionDeprecated::RegionDeprecated(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
|
||||||
Region(lmp, narg, arg)
|
|
||||||
{
|
{
|
||||||
std::string my_style = style;
|
std::string my_style = style;
|
||||||
|
|
||||||
if (my_style == "DEPRECATED") {
|
if (my_style == "DEPRECATED") {
|
||||||
if (lmp->comm->me == 0)
|
if (lmp->comm->me == 0) utils::logmesg(lmp, "\nRegion style 'DEPRECATED' is a dummy style\n\n");
|
||||||
utils::logmesg(lmp,"\nRegion style 'DEPRECATED' is a dummy style\n\n");
|
|
||||||
return;
|
return;
|
||||||
}
|
}
|
||||||
error->all(FLERR,"This region style is no longer available");
|
error->all(FLERR, "This region style is no longer available");
|
||||||
}
|
}
|
||||||
|
|||||||
@ -165,6 +165,7 @@ void Rerun::command(int narg, char **arg)
|
|||||||
modify->init();
|
modify->init();
|
||||||
update->integrate->setup_minimal(1);
|
update->integrate->setup_minimal(1);
|
||||||
modify->end_of_step();
|
modify->end_of_step();
|
||||||
|
output->next_dump_any = ntimestep;
|
||||||
if (firstflag) output->setup();
|
if (firstflag) output->setup();
|
||||||
else if (output->next) output->write(ntimestep);
|
else if (output->next) output->write(ntimestep);
|
||||||
|
|
||||||
|
|||||||
@ -1,4 +1,3 @@
|
|||||||
// clang-format off
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
https://www.lammps.org/, Sandia National Laboratories
|
||||||
@ -34,41 +33,39 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
void WriteDump::command(int narg, char **arg)
|
void WriteDump::command(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (narg < 3) error->all(FLERR,"Illegal write_dump command");
|
if (narg < 3) error->all(FLERR, "Illegal write_dump command");
|
||||||
|
|
||||||
// modindex = index in args of "modify" keyword
|
// modindex = index in args of "modify" keyword
|
||||||
// will be narg if "modify" is not present
|
// will be narg if "modify" is not present
|
||||||
|
|
||||||
int modindex;
|
int modindex;
|
||||||
for (modindex = 0; modindex < narg; modindex++)
|
for (modindex = 0; modindex < narg; modindex++)
|
||||||
if (strcmp(arg[modindex],"modify") == 0) break;
|
if (strcmp(arg[modindex], "modify") == 0) break;
|
||||||
|
|
||||||
// create the Dump instance
|
// create the Dump instance
|
||||||
// create dump command line with extra required args
|
// create dump command line with extra required args
|
||||||
|
|
||||||
auto dumpargs = new char*[modindex+2];
|
auto dumpargs = new char *[modindex + 2];
|
||||||
dumpargs[0] = (char *) "WRITE_DUMP"; // dump id
|
dumpargs[0] = (char *) "WRITE_DUMP"; // dump id
|
||||||
dumpargs[1] = arg[0]; // group
|
dumpargs[1] = arg[0]; // group
|
||||||
dumpargs[2] = arg[1]; // dump style
|
dumpargs[2] = arg[1]; // dump style
|
||||||
std::string ntimestep = std::to_string(MAX(update->ntimestep,1));
|
std::string ntimestep = std::to_string(MAX(update->ntimestep, 1));
|
||||||
dumpargs[3] = (char *) ntimestep.c_str(); // dump frequency
|
dumpargs[3] = (char *) ntimestep.c_str(); // dump frequency
|
||||||
|
|
||||||
for (int i = 2; i < modindex; ++i) dumpargs[i+2] = arg[i];
|
for (int i = 2; i < modindex; ++i) dumpargs[i + 2] = arg[i];
|
||||||
|
|
||||||
Dump *dump = output->add_dump(modindex+2, dumpargs);
|
Dump *dump = output->add_dump(modindex + 2, dumpargs);
|
||||||
if (modindex < narg) dump->modify_params(narg-modindex-1,&arg[modindex+1]);
|
if (modindex < narg) dump->modify_params(narg - modindex - 1, &arg[modindex + 1]);
|
||||||
|
|
||||||
// write out one frame and then delete the dump again
|
// write out one frame and then delete the dump again
|
||||||
// set multifile_override for DumpImage so that filename needs no "*"
|
// set multifile_override for DumpImage so that filename needs no "*"
|
||||||
|
|
||||||
if (strcmp(arg[1],"image") == 0)
|
if (strcmp(arg[1], "image") == 0) (dynamic_cast<DumpImage *>(dump))->multifile_override = 1;
|
||||||
(dynamic_cast<DumpImage *>( dump))->multifile_override = 1;
|
|
||||||
|
|
||||||
if (strcmp(arg[1],"cfg") == 0)
|
if (strcmp(arg[1], "cfg") == 0) (dynamic_cast<DumpCFG *>(dump))->multifile_override = 1;
|
||||||
(dynamic_cast<DumpCFG *>( dump))->multifile_override = 1;
|
|
||||||
|
|
||||||
if ((update->first_update == 0) && (comm->me == 0))
|
if ((update->first_update == 0) && (comm->me == 0))
|
||||||
error->warning(FLERR,"Calling write_dump before a full system init.");
|
error->warning(FLERR, "Calling write_dump before a full system init.");
|
||||||
|
|
||||||
dump->init();
|
dump->init();
|
||||||
dump->write();
|
dump->write();
|
||||||
|
|||||||
@ -4,8 +4,8 @@ From: ubuntu:22.04
|
|||||||
%post
|
%post
|
||||||
export DEBIAN_FRONTEND=noninteractive
|
export DEBIAN_FRONTEND=noninteractive
|
||||||
apt-get update
|
apt-get update
|
||||||
apt-get install --no-install-recommends -y software-properties-common
|
apt-get install --no-install-recommends -y software-properties-common gpg gpg-agent
|
||||||
# add-apt-repository ppa:openkim/latest
|
add-apt-repository ppa:openkim/latest
|
||||||
apt-get update
|
apt-get update
|
||||||
apt-get upgrade --no-install-recommends -y
|
apt-get upgrade --no-install-recommends -y
|
||||||
apt-get install --no-install-recommends -y \
|
apt-get install --no-install-recommends -y \
|
||||||
@ -74,29 +74,28 @@ From: ubuntu:22.04
|
|||||||
zstd \
|
zstd \
|
||||||
libyaml-cpp-dev \
|
libyaml-cpp-dev \
|
||||||
libkim-api-dev \
|
libkim-api-dev \
|
||||||
gpg-agent \
|
openkim-models
|
||||||
# openkim-models
|
|
||||||
|
|
||||||
# ###########################################################################
|
###########################################################################
|
||||||
# # KIM-API
|
# KIM-API
|
||||||
# ###########################################################################
|
###########################################################################
|
||||||
#
|
|
||||||
# # workaround for installing files in /usr/share/doc inside of a container
|
# workaround for installing files in /usr/share/doc inside of a container
|
||||||
# sed -i 's/path-exclude=\/usr\/share\/doc/#path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes
|
sed -i 's/path-exclude=\/usr\/share\/doc/#path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes
|
||||||
# apt-get install -y libkim-api-doc
|
apt-get install -y libkim-api-doc
|
||||||
# sed -i 's/#path-exclude=\/usr\/share\/doc/path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes
|
sed -i 's/#path-exclude=\/usr\/share\/doc/path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes
|
||||||
#
|
|
||||||
# # install KIM models
|
# install KIM models
|
||||||
# KIM_API_EXAMPLES=/usr/share/doc/libkim-api-dev/examples
|
KIM_API_EXAMPLES=/usr/share/doc/libkim-api-dev/examples
|
||||||
# gunzip $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003/LennardJones612_UniversalShifted.params.gz
|
# gunzip $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003/LennardJones612_UniversalShifted.params.gz
|
||||||
# gunzip $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ/ex_model_driver_P_LJ.f90.gz
|
# gunzip $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ/ex_model_driver_P_LJ.f90.gz
|
||||||
#
|
|
||||||
# kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/LennardJones612__MD_414112407348_003
|
kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/LennardJones612__MD_414112407348_003
|
||||||
# kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ
|
kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ
|
||||||
# kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones_Ar
|
kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones_Ar
|
||||||
# kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/ex_model_Ar_P_LJ
|
kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/ex_model_Ar_P_LJ
|
||||||
# kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003
|
kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003
|
||||||
# kim-api-collections-management install system $KIM_API_EXAMPLES/simulator-models/Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu
|
kim-api-collections-management install system $KIM_API_EXAMPLES/simulator-models/Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu
|
||||||
|
|
||||||
|
|
||||||
###########################################################################
|
###########################################################################
|
||||||
|
|||||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -46,9 +46,8 @@ target_link_libraries(test_dump_atom PRIVATE lammps GTest::GMock)
|
|||||||
add_test(NAME DumpAtom COMMAND test_dump_atom)
|
add_test(NAME DumpAtom COMMAND test_dump_atom)
|
||||||
set_tests_properties(DumpAtom PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
|
set_tests_properties(DumpAtom PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
|
||||||
|
|
||||||
if(PKG_COMPRESS)
|
find_program(GZIP_EXECUTABLE NAMES gzip)
|
||||||
find_program(GZIP_BINARY NAMES gzip REQUIRED)
|
if(PKG_COMPRESS AND GZIP_FOUND)
|
||||||
|
|
||||||
add_executable(test_dump_atom_compressed test_dump_atom_compressed.cpp compressed_dump_test_main.cpp)
|
add_executable(test_dump_atom_compressed test_dump_atom_compressed.cpp compressed_dump_test_main.cpp)
|
||||||
target_link_libraries(test_dump_atom_compressed PRIVATE lammps GTest::GMock)
|
target_link_libraries(test_dump_atom_compressed PRIVATE lammps GTest::GMock)
|
||||||
|
|
||||||
@ -65,39 +64,39 @@ if(PKG_COMPRESS)
|
|||||||
target_link_libraries(test_dump_xyz_compressed PRIVATE lammps GTest::GMock)
|
target_link_libraries(test_dump_xyz_compressed PRIVATE lammps GTest::GMock)
|
||||||
|
|
||||||
add_test(NAME DumpAtomGZ COMMAND test_dump_atom_compressed gz)
|
add_test(NAME DumpAtomGZ COMMAND test_dump_atom_compressed gz)
|
||||||
set_tests_properties(DumpAtomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}")
|
set_tests_properties(DumpAtomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_EXECUTABLE=${GZIP_EXECUTABLE}")
|
||||||
|
|
||||||
add_test(NAME DumpCustomGZ COMMAND test_dump_custom_compressed gz)
|
add_test(NAME DumpCustomGZ COMMAND test_dump_custom_compressed gz)
|
||||||
set_tests_properties(DumpCustomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}")
|
set_tests_properties(DumpCustomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_EXECUTABLE=${GZIP_EXECUTABLE}")
|
||||||
|
|
||||||
add_test(NAME DumpCfgGZ COMMAND test_dump_cfg_compressed gz)
|
add_test(NAME DumpCfgGZ COMMAND test_dump_cfg_compressed gz)
|
||||||
set_tests_properties(DumpCfgGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}")
|
set_tests_properties(DumpCfgGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_EXECUTABLE=${GZIP_EXECUTABLE}")
|
||||||
|
|
||||||
add_test(NAME DumpLocalGZ COMMAND test_dump_local_compressed gz)
|
add_test(NAME DumpLocalGZ COMMAND test_dump_local_compressed gz)
|
||||||
set_tests_properties(DumpLocalGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}")
|
set_tests_properties(DumpLocalGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_EXECUTABLE=${GZIP_EXECUTABLE}")
|
||||||
|
|
||||||
add_test(NAME DumpXYZGZ COMMAND test_dump_xyz_compressed gz)
|
add_test(NAME DumpXYZGZ COMMAND test_dump_xyz_compressed gz)
|
||||||
set_tests_properties(DumpXYZGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${GZIP_BINARY}")
|
set_tests_properties(DumpXYZGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_EXECUTABLE=${GZIP_EXECUTABLE}")
|
||||||
|
|
||||||
find_package(PkgConfig REQUIRED)
|
find_package(PkgConfig)
|
||||||
pkg_check_modules(Zstd IMPORTED_TARGET libzstd>=1.4)
|
pkg_check_modules(Zstd IMPORTED_TARGET libzstd>=1.4)
|
||||||
find_program(ZSTD_BINARY NAMES zstd)
|
find_program(ZSTD_EXECUTABLE NAMES zstd)
|
||||||
|
|
||||||
if(Zstd_FOUND AND ZSTD_BINARY)
|
if(Zstd_FOUND AND ZSTD_EXECUTABLE)
|
||||||
add_test(NAME DumpAtomZstd COMMAND test_dump_atom_compressed zstd)
|
add_test(NAME DumpAtomZstd COMMAND test_dump_atom_compressed zstd)
|
||||||
set_tests_properties(DumpAtomZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}")
|
set_tests_properties(DumpAtomZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_EXECUTABLE=${ZSTD_EXECUTABLE}")
|
||||||
|
|
||||||
add_test(NAME DumpCustomZstd COMMAND test_dump_custom_compressed zstd)
|
add_test(NAME DumpCustomZstd COMMAND test_dump_custom_compressed zstd)
|
||||||
set_tests_properties(DumpCustomZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}")
|
set_tests_properties(DumpCustomZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_EXECUTABLE=${ZSTD_EXECUTABLE}")
|
||||||
|
|
||||||
add_test(NAME DumpCfgZstd COMMAND test_dump_cfg_compressed zstd)
|
add_test(NAME DumpCfgZstd COMMAND test_dump_cfg_compressed zstd)
|
||||||
set_tests_properties(DumpCfgZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}")
|
set_tests_properties(DumpCfgZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_EXECUTABLE=${ZSTD_EXECUTABLE}")
|
||||||
|
|
||||||
add_test(NAME DumpLocalZstd COMMAND test_dump_local_compressed zstd)
|
add_test(NAME DumpLocalZstd COMMAND test_dump_local_compressed zstd)
|
||||||
set_tests_properties(DumpLocalZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}")
|
set_tests_properties(DumpLocalZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_EXECUTABLE=${ZSTD_EXECUTABLE}")
|
||||||
|
|
||||||
add_test(NAME DumpXYZZstd COMMAND test_dump_xyz_compressed zstd)
|
add_test(NAME DumpXYZZstd COMMAND test_dump_xyz_compressed zstd)
|
||||||
set_tests_properties(DumpXYZZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_BINARY=${ZSTD_BINARY}")
|
set_tests_properties(DumpXYZZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};COMPRESS_EXECUTABLE=${ZSTD_EXECUTABLE}")
|
||||||
endif()
|
endif()
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
@ -122,11 +121,11 @@ if(PKG_NETCDF)
|
|||||||
target_link_libraries(test_dump_netcdf PRIVATE lammps GTest::GMock)
|
target_link_libraries(test_dump_netcdf PRIVATE lammps GTest::GMock)
|
||||||
add_test(NAME DumpNetCDF COMMAND test_dump_netcdf)
|
add_test(NAME DumpNetCDF COMMAND test_dump_netcdf)
|
||||||
if(NOT (NCDUMP STREQUAL "NCDUMP-NOTFOUND"))
|
if(NOT (NCDUMP STREQUAL "NCDUMP-NOTFOUND"))
|
||||||
set_tests_properties(DumpNetCDF PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};NCDUMP_BINARY=${NCDUMP}")
|
set_tests_properties(DumpNetCDF PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};NCDUMP_EXECUTABLE=${NCDUMP}")
|
||||||
endif()
|
endif()
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
if(BUILD_TOOLS)
|
if(BUILD_TOOLS)
|
||||||
set_tests_properties(DumpAtom PROPERTIES ENVIRONMENT "BINARY2TXT_BINARY=$<TARGET_FILE:binary2txt>")
|
set_tests_properties(DumpAtom PROPERTIES ENVIRONMENT "BINARY2TXT_EXECUTABLE=$<TARGET_FILE:binary2txt>")
|
||||||
set_tests_properties(DumpCustom PROPERTIES ENVIRONMENT "BINARY2TXT_BINARY=$<TARGET_FILE:binary2txt>")
|
set_tests_properties(DumpCustom PROPERTIES ENVIRONMENT "BINARY2TXT_EXECUTABLE=$<TARGET_FILE:binary2txt>")
|
||||||
endif()
|
endif()
|
||||||
|
|||||||
@ -19,7 +19,7 @@
|
|||||||
|
|
||||||
extern const char *COMPRESS_SUFFIX;
|
extern const char *COMPRESS_SUFFIX;
|
||||||
extern const char *COMPRESS_EXTENSION;
|
extern const char *COMPRESS_EXTENSION;
|
||||||
extern char *COMPRESS_BINARY;
|
extern char *COMPRESS_EXECUTABLE;
|
||||||
|
|
||||||
class CompressedDumpTest : public MeltTest {
|
class CompressedDumpTest : public MeltTest {
|
||||||
protected:
|
protected:
|
||||||
@ -102,7 +102,7 @@ public:
|
|||||||
BEGIN_HIDE_OUTPUT();
|
BEGIN_HIDE_OUTPUT();
|
||||||
std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.'));
|
std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.'));
|
||||||
std::string cmdline =
|
std::string cmdline =
|
||||||
fmt::format("{} -d -c {} > {}", COMPRESS_BINARY, compressed_file, converted_file);
|
fmt::format("\"{}\" -d -c {} > {}", COMPRESS_EXECUTABLE, compressed_file, converted_file);
|
||||||
system(cmdline.c_str());
|
system(cmdline.c_str());
|
||||||
END_HIDE_OUTPUT();
|
END_HIDE_OUTPUT();
|
||||||
return converted_file;
|
return converted_file;
|
||||||
|
|||||||
@ -22,7 +22,7 @@
|
|||||||
|
|
||||||
const char *COMPRESS_SUFFIX = nullptr;
|
const char *COMPRESS_SUFFIX = nullptr;
|
||||||
const char *COMPRESS_EXTENSION = nullptr;
|
const char *COMPRESS_EXTENSION = nullptr;
|
||||||
char *COMPRESS_BINARY = nullptr;
|
char *COMPRESS_EXECUTABLE = nullptr;
|
||||||
bool verbose = false;
|
bool verbose = false;
|
||||||
|
|
||||||
int main(int argc, char **argv)
|
int main(int argc, char **argv)
|
||||||
@ -46,7 +46,7 @@ int main(int argc, char **argv)
|
|||||||
return 1;
|
return 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
COMPRESS_BINARY = getenv("COMPRESS_BINARY");
|
COMPRESS_EXECUTABLE = getenv("COMPRESS_EXECUTABLE");
|
||||||
|
|
||||||
// handle arguments passed via environment variable
|
// handle arguments passed via environment variable
|
||||||
if (const char *var = getenv("TEST_ARGS")) {
|
if (const char *var = getenv("TEST_ARGS")) {
|
||||||
|
|||||||
@ -2123,7 +2123,7 @@ TEST_F(AtomStyleTest, body_nparticle)
|
|||||||
"12.0 0.0 12.0 0.0 0.0 0.0\n"
|
"12.0 0.0 12.0 0.0 0.0 0.0\n"
|
||||||
"0.0 1.0 0.0\n"
|
"0.0 1.0 0.0\n"
|
||||||
"0.0 -3.0 0.0\n";
|
"0.0 -3.0 0.0\n";
|
||||||
FILE *fp = fopen("input_atom_styles.data", "w");
|
FILE *fp = fopen("input_atom_styles.data", "w");
|
||||||
fputs(data_file, fp);
|
fputs(data_file, fp);
|
||||||
fclose(fp);
|
fclose(fp);
|
||||||
BEGIN_HIDE_OUTPUT();
|
BEGIN_HIDE_OUTPUT();
|
||||||
@ -5159,7 +5159,7 @@ TEST_F(AtomStyleTest, oxdna)
|
|||||||
EXPECT_NEAR(bonus[9].shape[1], 0.5869922515711705, EPSILON);
|
EXPECT_NEAR(bonus[9].shape[1], 0.5869922515711705, EPSILON);
|
||||||
EXPECT_NEAR(bonus[9].shape[2], 0.5869922515711705, EPSILON);
|
EXPECT_NEAR(bonus[9].shape[2], 0.5869922515711705, EPSILON);
|
||||||
|
|
||||||
EXPECT_NEAR(bonus[0].quat[0], 0.9890278201757743, EPSILON);
|
EXPECT_NEAR(bonus[0].quat[0], 0.9890278201757743, EPSILON);
|
||||||
EXPECT_NEAR(bonus[0].quat[1], 0.01779228232037064, EPSILON);
|
EXPECT_NEAR(bonus[0].quat[1], 0.01779228232037064, EPSILON);
|
||||||
EXPECT_NEAR(bonus[0].quat[2], -0.14337734159225404, EPSILON);
|
EXPECT_NEAR(bonus[0].quat[2], -0.14337734159225404, EPSILON);
|
||||||
EXPECT_NEAR(bonus[0].quat[3], 0.030827642240801516, EPSILON);
|
EXPECT_NEAR(bonus[0].quat[3], 0.030827642240801516, EPSILON);
|
||||||
@ -5246,7 +5246,6 @@ TEST_F(AtomStyleTest, oxdna)
|
|||||||
ASSERT_EQ(id5p[GETIDX(10)], -1);
|
ASSERT_EQ(id5p[GETIDX(10)], -1);
|
||||||
|
|
||||||
END_HIDE_OUTPUT();
|
END_HIDE_OUTPUT();
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
} // namespace LAMMPS_NS
|
} // namespace LAMMPS_NS
|
||||||
|
|||||||
@ -25,8 +25,8 @@
|
|||||||
|
|
||||||
using ::testing::Eq;
|
using ::testing::Eq;
|
||||||
|
|
||||||
char *BINARY2TXT_BINARY = nullptr;
|
char *BINARY2TXT_EXECUTABLE = nullptr;
|
||||||
bool verbose = false;
|
bool verbose = false;
|
||||||
|
|
||||||
class DumpAtomTest : public MeltTest {
|
class DumpAtomTest : public MeltTest {
|
||||||
std::string dump_style = "atom";
|
std::string dump_style = "atom";
|
||||||
@ -100,7 +100,7 @@ public:
|
|||||||
std::string convert_binary_to_text(std::string binary_file)
|
std::string convert_binary_to_text(std::string binary_file)
|
||||||
{
|
{
|
||||||
BEGIN_HIDE_OUTPUT();
|
BEGIN_HIDE_OUTPUT();
|
||||||
std::string cmdline = fmt::format("{} {}", BINARY2TXT_BINARY, binary_file);
|
std::string cmdline = fmt::format("\"{}\" {}", BINARY2TXT_EXECUTABLE, binary_file);
|
||||||
system(cmdline.c_str());
|
system(cmdline.c_str());
|
||||||
END_HIDE_OUTPUT();
|
END_HIDE_OUTPUT();
|
||||||
return fmt::format("{}.txt", binary_file);
|
return fmt::format("{}.txt", binary_file);
|
||||||
@ -328,7 +328,7 @@ TEST_F(DumpAtomTest, triclinic_with_image_run0)
|
|||||||
|
|
||||||
TEST_F(DumpAtomTest, binary_run0)
|
TEST_F(DumpAtomTest, binary_run0)
|
||||||
{
|
{
|
||||||
if (!BINARY2TXT_BINARY) GTEST_SKIP();
|
if (!BINARY2TXT_EXECUTABLE) GTEST_SKIP();
|
||||||
|
|
||||||
auto text_file = text_dump_filename("run0");
|
auto text_file = text_dump_filename("run0");
|
||||||
auto binary_file = binary_dump_filename("run0");
|
auto binary_file = binary_dump_filename("run0");
|
||||||
@ -349,7 +349,7 @@ TEST_F(DumpAtomTest, binary_run0)
|
|||||||
|
|
||||||
TEST_F(DumpAtomTest, binary_with_units_run0)
|
TEST_F(DumpAtomTest, binary_with_units_run0)
|
||||||
{
|
{
|
||||||
if (!BINARY2TXT_BINARY) GTEST_SKIP();
|
if (!BINARY2TXT_EXECUTABLE) GTEST_SKIP();
|
||||||
|
|
||||||
auto text_file = text_dump_filename("with_units_run0");
|
auto text_file = text_dump_filename("with_units_run0");
|
||||||
auto binary_file = binary_dump_filename("with_units_run0");
|
auto binary_file = binary_dump_filename("with_units_run0");
|
||||||
@ -370,7 +370,7 @@ TEST_F(DumpAtomTest, binary_with_units_run0)
|
|||||||
|
|
||||||
TEST_F(DumpAtomTest, binary_with_time_run0)
|
TEST_F(DumpAtomTest, binary_with_time_run0)
|
||||||
{
|
{
|
||||||
if (!BINARY2TXT_BINARY) GTEST_SKIP();
|
if (!BINARY2TXT_EXECUTABLE) GTEST_SKIP();
|
||||||
|
|
||||||
auto text_file = text_dump_filename("with_time_run0");
|
auto text_file = text_dump_filename("with_time_run0");
|
||||||
auto binary_file = binary_dump_filename("with_time_run0");
|
auto binary_file = binary_dump_filename("with_time_run0");
|
||||||
@ -391,7 +391,7 @@ TEST_F(DumpAtomTest, binary_with_time_run0)
|
|||||||
|
|
||||||
TEST_F(DumpAtomTest, binary_triclinic_run0)
|
TEST_F(DumpAtomTest, binary_triclinic_run0)
|
||||||
{
|
{
|
||||||
if (!BINARY2TXT_BINARY) GTEST_SKIP();
|
if (!BINARY2TXT_EXECUTABLE) GTEST_SKIP();
|
||||||
|
|
||||||
auto text_file = text_dump_filename("tri_run0");
|
auto text_file = text_dump_filename("tri_run0");
|
||||||
auto binary_file = binary_dump_filename("tri_run0");
|
auto binary_file = binary_dump_filename("tri_run0");
|
||||||
@ -413,7 +413,7 @@ TEST_F(DumpAtomTest, binary_triclinic_run0)
|
|||||||
|
|
||||||
TEST_F(DumpAtomTest, binary_triclinic_with_units_run0)
|
TEST_F(DumpAtomTest, binary_triclinic_with_units_run0)
|
||||||
{
|
{
|
||||||
if (!BINARY2TXT_BINARY) GTEST_SKIP();
|
if (!BINARY2TXT_EXECUTABLE) GTEST_SKIP();
|
||||||
|
|
||||||
auto text_file = text_dump_filename("tri_with_units_run0");
|
auto text_file = text_dump_filename("tri_with_units_run0");
|
||||||
auto binary_file = binary_dump_filename("tri_with_units_run0");
|
auto binary_file = binary_dump_filename("tri_with_units_run0");
|
||||||
@ -435,7 +435,7 @@ TEST_F(DumpAtomTest, binary_triclinic_with_units_run0)
|
|||||||
|
|
||||||
TEST_F(DumpAtomTest, binary_triclinic_with_time_run0)
|
TEST_F(DumpAtomTest, binary_triclinic_with_time_run0)
|
||||||
{
|
{
|
||||||
if (!BINARY2TXT_BINARY) GTEST_SKIP();
|
if (!BINARY2TXT_EXECUTABLE) GTEST_SKIP();
|
||||||
|
|
||||||
auto text_file = text_dump_filename("tri_with_time_run0");
|
auto text_file = text_dump_filename("tri_with_time_run0");
|
||||||
auto binary_file = binary_dump_filename("tri_with_time_run0");
|
auto binary_file = binary_dump_filename("tri_with_time_run0");
|
||||||
@ -457,7 +457,7 @@ TEST_F(DumpAtomTest, binary_triclinic_with_time_run0)
|
|||||||
|
|
||||||
TEST_F(DumpAtomTest, binary_triclinic_with_image_run0)
|
TEST_F(DumpAtomTest, binary_triclinic_with_image_run0)
|
||||||
{
|
{
|
||||||
if (!BINARY2TXT_BINARY) GTEST_SKIP();
|
if (!BINARY2TXT_EXECUTABLE) GTEST_SKIP();
|
||||||
|
|
||||||
auto text_file = text_dump_filename("tri_with_image_run0");
|
auto text_file = text_dump_filename("tri_with_image_run0");
|
||||||
auto binary_file = binary_dump_filename("tri_with_image_run0");
|
auto binary_file = binary_dump_filename("tri_with_image_run0");
|
||||||
@ -649,7 +649,7 @@ TEST_F(DumpAtomTest, write_dump)
|
|||||||
|
|
||||||
TEST_F(DumpAtomTest, binary_write_dump)
|
TEST_F(DumpAtomTest, binary_write_dump)
|
||||||
{
|
{
|
||||||
if (!BINARY2TXT_BINARY) GTEST_SKIP();
|
if (!BINARY2TXT_EXECUTABLE) GTEST_SKIP();
|
||||||
|
|
||||||
auto reference = binary_dump_filename("write_run0_ref");
|
auto reference = binary_dump_filename("write_run0_ref");
|
||||||
auto dump_file = fmt::format("write_{}", binary_dump_filename("write_dump_atom_run*_p%"));
|
auto dump_file = fmt::format("write_{}", binary_dump_filename("write_dump_atom_run*_p%"));
|
||||||
@ -693,7 +693,7 @@ int main(int argc, char **argv)
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
BINARY2TXT_BINARY = getenv("BINARY2TXT_BINARY");
|
BINARY2TXT_EXECUTABLE = getenv("BINARY2TXT_EXECUTABLE");
|
||||||
|
|
||||||
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
|
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
|
||||||
|
|
||||||
|
|||||||
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Reference in New Issue
Block a user