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

This commit is contained in:
Axel Kohlmeyer 2021-04-26 13:27:58 -04:00
parent e9e0bb71b6 31d244dd80
commit 6b04ebd617
No known key found for this signature in database
GPG Key ID: D9B44E93BF0C375A
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)
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)
enable_language(C)
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
)
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" CACHE STRING "URL for MathJax tarball")
set(MATHJAX_MD5 "a4a6a093a89bc2ccab1452d766b98e53" CACHE STRING "MD5 checksum of 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 "d1c98c746888bfd52ca8ebc10704f92f" CACHE STRING "MD5 checksum of MathJax tarball")
mark_as_advanced(MATHJAX_URL)
# 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()
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}
-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})
get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
@ -289,18 +289,18 @@ elseif(GPU_API STREQUAL "HIP")
if(HIP_COMPILER STREQUAL "clang")
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}
COMMENT "Generating ${CU_NAME}.cubin")
else()
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}
COMMENT "Generating ${CU_NAME}.cubin")
endif()
elseif(HIP_PLATFORM STREQUAL "nvcc")
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}
COMMENT "Generating ${CU_NAME}.cubin")
endif()

2
cmake/Modules/Packages/USER-PACE.cmake
View File

@ -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)
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_link_libraries(lammps PRIVATE pace)

73
cmake/Modules/Testing.cmake
View File

@ -56,3 +56,76 @@ if(ENABLE_TESTING)
get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
endif()
# Compiler specific features for testing
if(${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
View File

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

20
cmake/presets/all_on.cmake
View File

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

2
doc/Makefile
View File

@ -236,7 +236,7 @@ $(VENV):
)
$(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)
@( \

20
doc/src/Developer_utils.rst
View File

@ -12,11 +12,18 @@ reduces redundant implementations and encourages consistent behavior.
I/O with status check
^^^^^^^^^^^^^^^^^^^^^
These are wrappers around the corresponding C library calls like
``fgets()`` or ``fread()``. They will check if there were errors
on reading or an unexpected end-of-file state was reached. In that
case, the functions will stop the calculation with an error message,
indicating the name of the problematic file, if possible.
The the first two functions are wrappers around the corresponding C
library calls ``fgets()`` or ``fread()``. They will check if there
were errors on reading or an unexpected end-of-file state was reached.
In that case, the functions will stop with an error message, indicating
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
:project: progguide
.. doxygenfunction:: read_lines_from_file
:project: progguide
----------
String to number conversions with validity check

16
doc/src/fix_precession_spin.rst
View File

@ -125,10 +125,10 @@ axis along the :math:`(1 1 1)`-type cube diagonals). :math:`K_2^c >
diagonals. See chapter 2 of :ref:`(Skomski) <Skomski1>` for more
details on cubic anisotropies.
Style *stt* is used to simulate the interaction between the spins and
Style *stt* is used to simulate the interaction between the spins and
a spin-transfer torque.
See equation (7) of :ref:`(Chirac) <Chirac1>` for more details about the
implemented spin-transfer torque term.
See equation (7) of :ref:`(Chirac) <Chirac1>` for more details about the
implemented spin-transfer torque term.
In all cases, the choice of :math:`(x y z)` only imposes the vector
directions for the forces. Only the direction of the vector is
@ -139,12 +139,12 @@ Those styles can be combined within one single command line.
.. note::
The norm of all vectors defined with the precession/spin command
The norm of all vectors defined with the precession/spin command
have to be non-zero. For example, defining
"fix 1 all precession/spin zeeman 0.1 0.0 0.0 0.0" would result
in an error message.
in an error message.
Since those vector components are used to compute the inverse of the
field (or anisotropy) vector norm, setting a zero-vector would result
field (or anisotropy) vector norm, setting a zero-vector would result
in a division by zero.
----------
@ -197,6 +197,6 @@ Oxford University Press.
.. _Chirac1:
**(Chirac)** Chirac, Théophile, et al. Ultrafast antiferromagnetic
switching in NiO induced by spin transfer torques.
**(Chirac)** Chirac, Theophile, et al. Ultrafast antiferromagnetic
switching in NiO induced by spin transfer torques.
Physical Review B 102.13 (2020): 134415.

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

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

4
lib/atc/LammpsInterface.cpp
View File

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

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

@ -108,17 +108,14 @@ class UCL_Program {
std::cerr << log << std::endl
<< "----------------------------------------------------------\n\n";
#endif
if (foutput != NULL) {
fprintf(foutput,"\n\n");
fprintf(foutput,
"----------------------------------------------------------\n");
fprintf(foutput," UCL Error: Error compiling PTX Program...\n");
fprintf(foutput,
"----------------------------------------------------------\n");
fprintf(foutput,"%s\n",log);
fprintf(foutput,
"----------------------------------------------------------\n");
fprintf(foutput,"\n\n");
if (foutput != nullptr) {
fprintf(foutput,"\n\n");
fprintf(foutput, "----------------------------------------------------------\n");
fprintf(foutput, " UCL Error: Error compiling PTX Program...\n");
fprintf(foutput, "----------------------------------------------------------\n");
fprintf(foutput, "%s\n",log->c_str());
fprintf(foutput, "----------------------------------------------------------\n");
fprintf(foutput,"\n\n");
}
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 << " Type of device: "
<< 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: ";
if (is_subdevice(i))
out << "Yes\n";
@ -796,6 +799,16 @@ void UCL_Device::print_all(std::ostream &out) {
out << "Yes\n";
else
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;
#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);
#if defined(LAL_OCL_EV_JIT)
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;
#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);
#if defined(LAL_OCL_EV_JIT)
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;
#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);
#if defined(LAL_OCL_EV_JIT)
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;
#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);
#if defined(LAL_OCL_EV_JIT)
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;
#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);
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));

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;
#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);
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));

4
lib/gpu/lal_neighbor.h
View File

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

4
lib/gpu/lal_neighbor_gpu.cu
View File

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

2
src/ASPHERE/compute_erotate_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/compute_temp_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nh_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nph_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_npt_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nve_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nve_asphere_noforce.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nve_line.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nve_tri.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/fix_nvt_asphere.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/pair_gayberne.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/pair_line_lj.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/pair_resquared.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/ASPHERE/pair_tri_lj.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/body_nparticle.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/body_rounded_polygon.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/body_rounded_polyhedron.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/compute_body_local.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/compute_temp_body.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/fix_nh_body.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
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 "error.h"
#include "group.h"
#include "modify.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

2
src/BODY/fix_nph_body.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
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 "error.h"
#include "group.h"
#include "modify.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

2
src/BODY/fix_npt_body.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/fix_nve_body.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
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 "modify.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

2
src/BODY/fix_nvt_body.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
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 <cmath>
#include <cstring>
#include "atom.h"
#include "atom_vec_body.h"
#include "body_rounded_polygon.h"
#include "domain.h"
#include "update.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "math_extra.h"
#include "memory.h"
#include "error.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

2
src/BODY/fix_wall_body_polygon.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/fix_wall_body_polyhedron.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
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 <cmath>
#include <cstring>
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_body.h"
#include "body_nparticle.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.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;

2
src/BODY/pair_body_nparticle.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/pair_body_rounded_polygon.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/BODY/pair_body_rounded_polyhedron.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CLASS2/angle_class2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CLASS2/bond_class2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CLASS2/dihedral_class2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CLASS2/improper_class2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CLASS2/pair_lj_class2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract
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++ -*- ----------------------------------------------------------
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
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++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/fix_wall_colloid.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_brownian.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_brownian_poly.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_colloid.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_lubricate.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_lubricateU.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_lubricateU_poly.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COLLOID/pair_lubricate_poly.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
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 <cmath>
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "error.h"
#include "force.h"
#include "neigh_list.h"
#include "neighbor.h"
#include <cmath>
using namespace LAMMPS_NS;

2
src/COLLOID/pair_yukawa_colloid.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_atom_gz.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_atom_zstd.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_cfg_gz.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_cfg_zstd.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_custom_gz.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_custom_zstd.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_local_gz.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_local_zstd.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_xyz_gz.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/COMPRESS/dump_xyz_zstd.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

7
src/COMPRESS/gz_file_writer.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -19,9 +19,10 @@
#define LMP_GZ_FILE_WRITER_H
#include "file_writer.h"
#include <exception>
#include <string>
#include <zlib.h>
#include <exception>
namespace LAMMPS_NS {
@ -40,8 +41,6 @@ public:
void setCompressionLevel(int level);
};
}
#endif

6
src/COMPRESS/zstd_file_writer.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -21,9 +21,9 @@
#define LMP_ZSTD_FILE_WRITER_H
#include "file_writer.h"
#include <string>
#include <zstd.h>
#include <exception>
namespace LAMMPS_NS {
@ -47,8 +47,6 @@ public:
void setCompressionLevel(int level);
void setChecksum(bool enabled);
};
}
#endif

2
src/CORESHELL/compute_temp_cs.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CORESHELL/pair_born_coul_dsf_cs.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CORESHELL/pair_born_coul_long_cs.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
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
http://lammps.sandia.gov, Sandia National Laboratories
https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CORESHELL/pair_coul_long_cs.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CORESHELL/pair_coul_wolf_cs.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
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++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/CORESHELL/pair_lj_cut_coul_long_cs.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/DIPOLE/atom_vec_dipole.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/DIPOLE/pair_lj_cut_dipole_cut.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/DIPOLE/pair_lj_long_dipole_long.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/GPU/fix_gpu.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
src/GPU/fix_nh_gpu.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
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
Copyright (2003) Sandia Corporation. Under the terms of Contract

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