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Merge branch 'master' into varargs-log-error-functions

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This commit is contained in:
Axel Kohlmeyer
2021-04-26 13:27:58 -04:00
parent e9e0bb71b6 31d244dd80
commit 6b04ebd617
1845 changed files with 3369 additions and 3357 deletions
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63
cmake/CMakeLists.txt
View File

@ -245,69 +245,6 @@ if(BUILD_OMP)
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX) target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
endif() endif()
# Compiler specific features for testing
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE)
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
endif()
else()
target_compile_options(lammps PUBLIC --coverage)
target_link_options(lammps PUBLIC --coverage)
endif()
endif()
endif()
#######################################
# add custom target for IWYU analysis
#######################################
set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
mark_as_advanced(ENABLE_IWYU)
if(ENABLE_IWYU)
set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
find_program(IWYU_EXE NAMES include-what-you-use iwyu)
find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
if (IWYU_EXE AND IWYU_TOOL)
add_custom_target(
iwyu
${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp
COMMENT "Running IWYU")
add_dependencies(iwyu lammps)
else()
message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
"and the iwyu-tool/iwyu_tool script installed in your PATH")
endif()
endif()
set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
mark_as_advanced(ENABLE_SANITIZER)
set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
if(NOT ENABLE_SANITIZER STREQUAL "none")
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
endif()
else()
target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
endif()
else()
message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
set(ENABLE_SANITIZER "none")
endif()
endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
enable_language(C) enable_language(C)
find_package(LAPACK) find_package(LAPACK)

4
cmake/Modules/Documentation.cmake
View File

@ -55,8 +55,8 @@ if(BUILD_DOC)
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
) )
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" CACHE STRING "URL for MathJax tarball") set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
set(MATHJAX_MD5 "a4a6a093a89bc2ccab1452d766b98e53" CACHE STRING "MD5 checksum of MathJax tarball") set(MATHJAX_MD5 "d1c98c746888bfd52ca8ebc10704f92f" CACHE STRING "MD5 checksum of MathJax tarball")
mark_as_advanced(MATHJAX_URL) mark_as_advanced(MATHJAX_URL)
# download mathjax distribution and unpack to folder "mathjax" # download mathjax distribution and unpack to folder "mathjax"

10
cmake/Modules/Packages/GPU.cmake
View File

@ -112,10 +112,10 @@ if(GPU_API STREQUAL "CUDA")
endif() endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC} cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING}) -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC} cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING}) -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
foreach(CU_OBJ ${GPU_GEN_OBJS}) foreach(CU_OBJ ${GPU_GEN_OBJS})
get_filename_component(CU_NAME ${CU_OBJ} NAME_WE) get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
@ -289,18 +289,18 @@ elseif(GPU_API STREQUAL "HIP")
if(HIP_COMPILER STREQUAL "clang") if(HIP_COMPILER STREQUAL "clang")
add_custom_command(OUTPUT ${CUBIN_FILE} add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE} VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE} DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin") COMMENT "Generating ${CU_NAME}.cubin")
else() else()
add_custom_command(OUTPUT ${CUBIN_FILE} add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE} VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE} DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin") COMMENT "Generating ${CU_NAME}.cubin")
endif() endif()
elseif(HIP_PLATFORM STREQUAL "nvcc") elseif(HIP_PLATFORM STREQUAL "nvcc")
add_custom_command(OUTPUT ${CUBIN_FILE} add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE} VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
DEPENDS ${CU_FILE} DEPENDS ${CU_FILE}
COMMENT "Generating ${CU_NAME}.cubin") COMMENT "Generating ${CU_NAME}.cubin")
endif() endif()

2
cmake/Modules/Packages/USER-PACE.cmake
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@ -20,7 +20,7 @@ file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PAC
list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp) list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
add_library(pace STATIC ${PACE_EVALUATOR_SOURCES}) add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
set_target_properties(pace PROPERTIES OUTPUT_NAME pace${LAMMPS_MACHINE}) set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE pace) target_link_libraries(lammps PRIVATE pace)

73
cmake/Modules/Testing.cmake
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@ -56,3 +56,76 @@ if(ENABLE_TESTING)
get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE) get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN}) add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
endif() endif()
# Compiler specific features for testing
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE)
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
endif()
else()
target_compile_options(lammps PUBLIC --coverage)
target_link_options(lammps PUBLIC --coverage)
endif()
endif()
endif()
#######################################
# add custom target for IWYU analysis
#######################################
set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
mark_as_advanced(ENABLE_IWYU)
if(ENABLE_IWYU)
# enforce these settings
set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL "Enable reporting compilation commands to compile_commands.json" FORCE)
if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")))
message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers")
endif()
# detect the "native" header folder so we can include them first
execute_process(COMMAND ${CMAKE_CXX_COMPILER} --print-search-dirs OUTPUT_VARIABLE IWYU_SEARCH_PATHS)
string(REGEX REPLACE ".*libraries: *=([^:]+):.*" "\\1/include" IWYU_EXTRA_INCLUDE_DIR ${IWYU_SEARCH_PATHS})
find_program(IWYU_EXE NAMES include-what-you-use iwyu)
find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
if (IWYU_EXE AND IWYU_TOOL)
add_custom_target(
iwyu
${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -I${IWYU_EXTRA_INCLUDE_DIR} -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp
COMMENT "Running IWYU")
add_dependencies(iwyu lammps)
else()
message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
"and the iwyu-tool/iwyu_tool script installed in your PATH")
endif()
endif()
#######################################
# select code sanitizer options
#######################################
set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
mark_as_advanced(ENABLE_SANITIZER)
set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
if(NOT ENABLE_SANITIZER STREQUAL "none")
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
if(CMAKE_VERSION VERSION_LESS 3.13)
if(CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
endif()
else()
target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
endif()
else()
message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
set(ENABLE_SANITIZER "none")
endif()
endif()

20
cmake/presets/all_off.cmake
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@ -2,16 +2,16 @@
# an existing package selection without losing any other settings # an existing package selection without losing any other settings
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SNAP SPIN SRD VORONOI SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES}) foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE) set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

20
cmake/presets/all_on.cmake
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@ -4,16 +4,16 @@
# with just a working C++ compiler and an MPI library. # with just a working C++ compiler and an MPI library.
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SNAP SPIN SRD VORONOI SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF) USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES}) foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE) set(PKG_${PKG} ON CACHE BOOL "" FORCE)

9
cmake/presets/nolib.cmake
View File

@ -1,10 +1,11 @@
# preset that turns off all packages that require some form of external # preset that turns off all packages that require some form of external
# library or special compiler (fortran or cuda) or equivalent. # library or special compiler (fortran or cuda) or equivalent.
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB PYTHON VORONOI
USER-MOLFILE USER-MESONT USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB USER-MOLFILE USER-MESONT
USER-SCAFACOS USER-SMD USER-VTK) USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS
USER-SMD USER-VTK)
foreach(PKG ${PACKAGES_WITH_LIB}) foreach(PKG ${PACKAGES_WITH_LIB})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE) set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

2
doc/Makefile
View File

@ -236,7 +236,7 @@ $(VENV):
) )
$(MATHJAX): $(MATHJAX):
@git clone --depth 1 git://github.com/mathjax/MathJax.git $@ @git clone -b 3.1.4 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
$(TXT2RST) $(ANCHORCHECK): $(VENV) $(TXT2RST) $(ANCHORCHECK): $(VENV)
@( \ @( \

20
doc/src/Developer_utils.rst
View File

@ -12,11 +12,18 @@ reduces redundant implementations and encourages consistent behavior.
I/O with status check I/O with status check
^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^
These are wrappers around the corresponding C library calls like The the first two functions are wrappers around the corresponding C
``fgets()`` or ``fread()``. They will check if there were errors library calls ``fgets()`` or ``fread()``. They will check if there
on reading or an unexpected end-of-file state was reached. In that were errors on reading or an unexpected end-of-file state was reached.
case, the functions will stop the calculation with an error message, In that case, the functions will stop with an error message, indicating
indicating the name of the problematic file, if possible. the name of the problematic file, if possible unless the *error* argument
is a NULL pointer.
The :cpp:func:`read_lines_from_file` function will read the requested
number of lines of a maximum length into a buffer and will return 0
if successful or 1 if not. It also guarantees that all lines are
terminated with a newline character and the entire buffer with a
NULL character.
---------- ----------
@ -26,6 +33,9 @@ indicating the name of the problematic file, if possible.
.. doxygenfunction:: sfread .. doxygenfunction:: sfread
:project: progguide :project: progguide
.. doxygenfunction:: read_lines_from_file
:project: progguide
---------- ----------
String to number conversions with validity check String to number conversions with validity check

2
doc/src/fix_precession_spin.rst
View File

@ -197,6 +197,6 @@ Oxford University Press.
.. _Chirac1: .. _Chirac1:
**(Chirac)** Chirac, Théophile, et al. Ultrafast antiferromagnetic **(Chirac)** Chirac, Theophile, et al. Ultrafast antiferromagnetic
switching in NiO induced by spin transfer torques. switching in NiO induced by spin transfer torques.
Physical Review B 102.13 (2020): 134415. Physical Review B 102.13 (2020): 134415.

7
doc/utils/sphinx-config/false_positives.txt
View File

@ -101,6 +101,7 @@ anisotropic
anisotropies anisotropies
anisotropy anisotropy
ansi ansi
antiferromagnetic
antiquewhite antiquewhite
Antisymmetrized Antisymmetrized
antisymmetry antisymmetry
@ -2177,6 +2178,7 @@ nimpropers
nimpropertypes nimpropertypes
Nimpropertype Nimpropertype
Ninteger Ninteger
NiO
Nissila Nissila
nist nist
nitride nitride
@ -2188,6 +2190,7 @@ nl
nlayers nlayers
nlen nlen
Nlines Nlines
nlines
nlo nlo
nlocal nlocal
Nlocal Nlocal
@ -2279,6 +2282,7 @@ Ntype
ntypes ntypes
Ntypes Ntypes
nucleotides nucleotides
nullptr
num num
numa numa
numactl numactl
@ -3163,6 +3167,7 @@ th
thb thb
thei thei
Theodorou Theodorou
Theophile
Theor Theor
thermalization thermalization
thermalize thermalize
@ -3315,6 +3320,7 @@ Uleft
uloop uloop
Ulomek Ulomek
ulsph ulsph
Ultrafast
uMech uMech
umin umin
Umin Umin
@ -3595,6 +3601,7 @@ ZBL
Zc Zc
zcm zcm
Zeeman Zeeman
zeeman
Zemer Zemer
Zepeda Zepeda
zflag zflag

4
lib/atc/LammpsInterface.cpp
View File

@ -26,6 +26,7 @@
#include "bond.h" // bond potentials #include "bond.h" // bond potentials
#include "comm.h" // #include "comm.h" //
#include "fix.h" #include "fix.h"
#include "utils.h"
// ATC includes // ATC includes
#include "ATC_Error.h" #include "ATC_Error.h"
@ -47,6 +48,7 @@ using std::pair;
using std::string; using std::string;
using std::set; using std::set;
using LAMMPS_NS::bigint; using LAMMPS_NS::bigint;
using LAMMPS_NS::utils::read_lines_from_file;
namespace ATC { namespace ATC {
@ -236,7 +238,7 @@ std::string LammpsInterface::read_file(std::string filename) const
std::stringstream s; std::stringstream s;
bool eof = false; bool eof = false;
while ( ! eof) { while ( ! eof) {
eof = lammps_->comm->read_lines_from_file(fp,1,MAXLINE,buffer); eof = read_lines_from_file(fp,1,MAXLINE,buffer,comm_rank(),lammps_->world);
s << buffer; s << buffer;
} }
fclose(fp); fclose(fp);

19
lib/gpu/geryon/nvd_kernel.h
View File

@ -108,17 +108,14 @@ class UCL_Program {
std::cerr << log << std::endl std::cerr << log << std::endl
<< "----------------------------------------------------------\n\n"; << "----------------------------------------------------------\n\n";
#endif #endif
if (foutput != NULL) { if (foutput != nullptr) {
fprintf(foutput,"\n\n"); fprintf(foutput,"\n\n");
fprintf(foutput, fprintf(foutput, "----------------------------------------------------------\n");
"----------------------------------------------------------\n"); fprintf(foutput, " UCL Error: Error compiling PTX Program...\n");
fprintf(foutput," UCL Error: Error compiling PTX Program...\n"); fprintf(foutput, "----------------------------------------------------------\n");
fprintf(foutput, fprintf(foutput, "%s\n",log->c_str());
"----------------------------------------------------------\n"); fprintf(foutput, "----------------------------------------------------------\n");
fprintf(foutput,"%s\n",log); fprintf(foutput,"\n\n");
fprintf(foutput,
"----------------------------------------------------------\n");
fprintf(foutput,"\n\n");
} }
return UCL_COMPILE_ERROR; return UCL_COMPILE_ERROR;
} }

13
lib/gpu/geryon/ocl_device.h
View File

@ -728,6 +728,9 @@ void UCL_Device::print_all(std::ostream &out) {
out << "\nDevice " << i << ": \"" << name(i).c_str() << "\"\n"; out << "\nDevice " << i << ": \"" << name(i).c_str() << "\"\n";
out << " Type of device: " out << " Type of device: "
<< device_type_name(i).c_str() << std::endl; << device_type_name(i).c_str() << std::endl;
out << " Supported OpenCL Version: "
<< _properties[i].cl_device_version / 100 << "."
<< _properties[i].cl_device_version % 100 << std::endl;
out << " Is a subdevice: "; out << " Is a subdevice: ";
if (is_subdevice(i)) if (is_subdevice(i))
out << "Yes\n"; out << "Yes\n";
@ -796,6 +799,16 @@ void UCL_Device::print_all(std::ostream &out) {
out << "Yes\n"; out << "Yes\n";
else else
out << "No\n"; out << "No\n";
out << " Subgroup support: ";
if (_properties[i].has_subgroup_support)
out << "Yes\n";
else
out << "No\n";
out << " Shuffle support: ";
if (_properties[i].has_shuffle_support)
out << "Yes\n";
else
out << "No\n";
} }
} }
} }

2
lib/gpu/lal_base_atomic.cpp
View File

@ -335,7 +335,7 @@ void BaseAtomicT::compile_kernels(UCL_Device &dev, const void *pair_str,
_compiled=true; _compiled=true;
#if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0))
if (dev.cl_device_version() >= 210) { if (dev.has_subgroup_support()) {
size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size); size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size);
#if defined(LAL_OCL_EV_JIT) #if defined(LAL_OCL_EV_JIT)
mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size));

2
lib/gpu/lal_base_charge.cpp
View File

@ -348,7 +348,7 @@ void BaseChargeT::compile_kernels(UCL_Device &dev, const void *pair_str,
_compiled=true; _compiled=true;
#if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0))
if (dev.cl_device_version() >= 210) { if (dev.has_subgroup_support()) {
size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size); size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size);
#if defined(LAL_OCL_EV_JIT) #if defined(LAL_OCL_EV_JIT)
mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size));

2
lib/gpu/lal_base_dipole.cpp
View File

@ -356,7 +356,7 @@ void BaseDipoleT::compile_kernels(UCL_Device &dev, const void *pair_str,
_compiled=true; _compiled=true;
#if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0))
if (dev.cl_device_version() >= 210) { if (dev.has_subgroup_support()) {
size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size); size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size);
#if defined(LAL_OCL_EV_JIT) #if defined(LAL_OCL_EV_JIT)
mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size));

2
lib/gpu/lal_base_dpd.cpp
View File

@ -356,7 +356,7 @@ void BaseDPDT::compile_kernels(UCL_Device &dev, const void *pair_str,
_compiled=true; _compiled=true;
#if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0))
if (dev.cl_device_version() >= 210) { if (dev.has_subgroup_support()) {
size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size); size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size);
#if defined(LAL_OCL_EV_JIT) #if defined(LAL_OCL_EV_JIT)
mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size)); mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size));

2
lib/gpu/lal_base_ellipsoid.cpp
View File

@ -554,7 +554,7 @@ void BaseEllipsoidT::compile_kernels(UCL_Device &dev,
_compiled=true; _compiled=true;
#if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0))
if (dev.cl_device_version() >= 210) { if (dev.has_subgroup_support()) {
size_t mx_subgroup_sz = k_lj_fast.max_subgroup_size(_block_size); size_t mx_subgroup_sz = k_lj_fast.max_subgroup_size(_block_size);
mx_subgroup_sz = std::min(mx_subgroup_sz, k_ellipsoid.max_subgroup_size(_block_size)); mx_subgroup_sz = std::min(mx_subgroup_sz, k_ellipsoid.max_subgroup_size(_block_size));
mx_subgroup_sz = std::min(mx_subgroup_sz, k_sphere_ellipsoid.max_subgroup_size(_block_size)); mx_subgroup_sz = std::min(mx_subgroup_sz, k_sphere_ellipsoid.max_subgroup_size(_block_size));

2
lib/gpu/lal_base_three.cpp
View File

@ -461,7 +461,7 @@ void BaseThreeT::compile_kernels(UCL_Device &dev, const void *pair_str,
_compiled=true; _compiled=true;
#if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)) #if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0))
if (dev.cl_device_version() >= 210) { if (dev.has_subgroup_support()) {
size_t mx_subgroup_sz = k_pair.max_subgroup_size(_block_size); size_t mx_subgroup_sz = k_pair.max_subgroup_size(_block_size);
mx_subgroup_sz = std::min(mx_subgroup_sz, k_three_center.max_subgroup_size(_block_size)); mx_subgroup_sz = std::min(mx_subgroup_sz, k_three_center.max_subgroup_size(_block_size));
mx_subgroup_sz = std::min(mx_subgroup_sz, k_three_end.max_subgroup_size(_block_size)); mx_subgroup_sz = std::min(mx_subgroup_sz, k_three_end.max_subgroup_size(_block_size));

4
lib/gpu/lal_neighbor.h
View File

@ -26,8 +26,8 @@
#if !defined(USE_OPENCL) && !defined(USE_HIP) #if !defined(USE_OPENCL) && !defined(USE_HIP)
#ifndef LAL_USE_OLD_NEIGHBOR #ifndef LAL_USE_OLD_NEIGHBOR
// Issue with incorrect results with CUDA 11.2 // Issue with incorrect results with CUDA >= 11.2
#if (CUDA_VERSION > 11019) && (CUDA_VERSION < 11030) #if (CUDA_VERSION > 11019)
#define LAL_USE_OLD_NEIGHBOR #define LAL_USE_OLD_NEIGHBOR
#endif #endif
#endif #endif

4
lib/gpu/lal_neighbor_gpu.cu
View File

@ -34,8 +34,8 @@ _texture_2d( pos_tex,int4);
#endif #endif
#ifdef NV_KERNEL #ifdef NV_KERNEL
#if (__CUDACC_VER_MAJOR__ == 11) && (__CUDACC_VER_MINOR__ == 2) #if (__CUDACC_VER_MAJOR__ == 11) && (__CUDACC_VER_MINOR__ >= 2)
// Issue with incorrect results in CUDA 11.2 // Issue with incorrect results in CUDA >= 11.2
#define LAL_USE_OLD_NEIGHBOR #define LAL_USE_OLD_NEIGHBOR
#endif #endif
#endif #endif

2
src/ASPHERE/compute_erotate_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/compute_temp_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nh_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nph_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_npt_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nve_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nve_asphere_noforce.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nve_line.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nve_tri.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nvt_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/pair_gayberne.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/pair_line_lj.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/pair_resquared.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/pair_tri_lj.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/body_nparticle.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/body_rounded_polygon.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/body_rounded_polyhedron.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/compute_body_local.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/compute_temp_body.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/fix_nh_body.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

3
src/BODY/fix_nph_body.cpp
View File

@ -18,11 +18,8 @@
#include "fix_nph_body.h" #include "fix_nph_body.h"
#include "error.h" #include "error.h"
#include "group.h"
#include "modify.h" #include "modify.h"
#include <cstring>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;

2
src/BODY/fix_nph_body.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

3
src/BODY/fix_npt_body.cpp
View File

@ -18,11 +18,8 @@
#include "fix_npt_body.h" #include "fix_npt_body.h"
#include "error.h" #include "error.h"
#include "group.h"
#include "modify.h" #include "modify.h"
#include <cstring>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;

2
src/BODY/fix_npt_body.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/fix_nve_body.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/fix_nvt_body.cpp
View File

@ -21,8 +21,6 @@
#include "group.h" #include "group.h"
#include "modify.h" #include "modify.h"
#include <cstring>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;

2
src/BODY/fix_nvt_body.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

10
src/BODY/fix_wall_body_polygon.cpp
View File

@ -16,18 +16,20 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "fix_wall_body_polygon.h" #include "fix_wall_body_polygon.h"
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"
#include "body_rounded_polygon.h" #include "body_rounded_polygon.h"
#include "domain.h" #include "domain.h"
#include "update.h" #include "error.h"
#include "force.h" #include "force.h"
#include "math_const.h" #include "math_const.h"
#include "math_extra.h" #include "math_extra.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;

2
src/BODY/fix_wall_body_polygon.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/fix_wall_body_polyhedron.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

15
src/BODY/pair_body_nparticle.cpp
View File

@ -12,18 +12,19 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_body_nparticle.h" #include "pair_body_nparticle.h"
#include <cmath>
#include <cstring>
#include "math_extra.h"
#include "atom.h" #include "atom.h"
#include "atom_vec_body.h" #include "atom_vec_body.h"
#include "body_nparticle.h" #include "body_nparticle.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h" #include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

2
src/BODY/pair_body_nparticle.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/pair_body_rounded_polygon.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/pair_body_rounded_polyhedron.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CLASS2/angle_class2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CLASS2/bond_class2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CLASS2/dihedral_class2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CLASS2/improper_class2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CLASS2/pair_lj_class2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

2
src/CLASS2/pair_lj_class2_coul_cut.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CLASS2/pair_lj_class2_coul_long.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/fix_wall_colloid.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_brownian.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_brownian_poly.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_colloid.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_lubricate.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_lubricateU.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_lubricateU_poly.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_lubricate_poly.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

11
src/COLLOID/pair_yukawa_colloid.cpp
View File

@ -16,13 +16,14 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_yukawa_colloid.h" #include "pair_yukawa_colloid.h"
#include <cmath>
#include "atom.h" #include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "error.h" #include "error.h"
#include "force.h"
#include "neigh_list.h"
#include "neighbor.h"
#include <cmath>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;

2
src/COLLOID/pair_yukawa_colloid.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_atom_gz.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_atom_zstd.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_cfg_gz.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_cfg_zstd.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_custom_gz.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_custom_zstd.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_local_gz.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_local_zstd.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_xyz_gz.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_xyz_zstd.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

7
src/COMPRESS/gz_file_writer.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -19,9 +19,10 @@
#define LMP_GZ_FILE_WRITER_H #define LMP_GZ_FILE_WRITER_H
#include "file_writer.h" #include "file_writer.h"
#include <exception>
#include <string> #include <string>
#include <zlib.h> #include <zlib.h>
#include <exception>
namespace LAMMPS_NS { namespace LAMMPS_NS {
@ -40,8 +41,6 @@ public:
void setCompressionLevel(int level); void setCompressionLevel(int level);
}; };
} }
#endif #endif

6
src/COMPRESS/zstd_file_writer.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -21,9 +21,9 @@
#define LMP_ZSTD_FILE_WRITER_H #define LMP_ZSTD_FILE_WRITER_H
#include "file_writer.h" #include "file_writer.h"
#include <string> #include <string>
#include <zstd.h> #include <zstd.h>
#include <exception>
namespace LAMMPS_NS { namespace LAMMPS_NS {
@ -47,8 +47,6 @@ public:
void setCompressionLevel(int level); void setCompressionLevel(int level);
void setChecksum(bool enabled); void setChecksum(bool enabled);
}; };
} }
#endif #endif

2
src/CORESHELL/compute_temp_cs.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CORESHELL/pair_born_coul_dsf_cs.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CORESHELL/pair_born_coul_long_cs.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

4
src/CORESHELL/pair_born_coul_wolf_cs.h
View File

@ -1,6 +1,6 @@
/* ---------------------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CORESHELL/pair_buck_coul_long_cs.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CORESHELL/pair_coul_long_cs.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CORESHELL/pair_coul_wolf_cs.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CORESHELL/pair_lj_class2_coul_long_cs.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CORESHELL/pair_lj_cut_coul_long_cs.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/DIPOLE/atom_vec_dipole.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/DIPOLE/pair_lj_cut_dipole_cut.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/DIPOLE/pair_lj_long_dipole_long.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/GPU/fix_gpu.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/GPU/fix_nh_gpu.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ---------------------------------------------------------- /* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract Copyright (2003) Sandia Corporation. Under the terms of Contract

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