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Merge branch 'collected-small-fixes' into lammps-gui

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# Conflicts:
#	cmake/CMakeLists.txt
This commit is contained in:
Axel Kohlmeyer
2023-08-01 03:07:56 -04:00
parent 418b2c3df0 b75407684f
commit 6b50daf5b7
17 changed files with 170 additions and 126 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
.github/CONTRIBUTING.md vendored
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@ -1,6 +1,6 @@
# Contributing to LAMMPS via GitHub
Thank your for considering to contribute to the LAMMPS software project.
Thank you for considering to contribute to the LAMMPS software project.
The following is a set of guidelines as well as explanations of policies and work flows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project.

20
cmake/CMakeLists.txt
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@ -796,9 +796,11 @@ include(Tools)
include(Documentation)
###############################################################################
# Install potential and force field files in data directory
# Install bench, potential and force field files in data directory
###############################################################################
set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_DATADIR}/lammps)
install(DIRECTORY ${LAMMPS_DIR}/bench DESTINATION ${LAMMPS_INSTALL_DATADIR})
install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR})
if(BUILD_TOOLS)
install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR})
@ -866,22 +868,6 @@ if(ClangFormat_FOUND)
WORKING_DIRECTORY ${LAMMPS_SOURCE_DIR})
endif()
# Packaging
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "LAMMPS")
set(CPACK_PACKAGE_VENDOR "The LAMMPS Developers")
set(CPACK_PACKAGE_NAME "LAMMPS")
set(CPACK_PACKAGE_VERSION "${PROJECT_VERSION}")
if(CPACK_GENERATOR STREQUAL "DragNDrop")
set(CPACK_DMG_VOLUME_NAME "LAMMPS-macOS-universal")
set(CPACK_DMG_BACKGROUND_IMAGE "${LAMMPS_DIR}/cmake/packaging/LAMMPS_DMG_BACKGROUND")
set(CPACK_DS_STORE_SETUP_SCRIPT "${LAMMPS_DIR}/cmake/packaging/LAMMPS_DMG_Setup.scpt")
set(CPACK_COMPONENTS_GROUPING ALL_COMPONENTS_IN_ONE)
install(FILES ${LAMMPS_DIR/cmake/packaging/README.macos DESTINATION . RENAME README.txt)
endif()
include(CPack)
# extract Kokkos compilation settings
get_cmake_property(_allvars VARIABLES)
foreach(_var ${_allvars})

4
cmake/Modules/Packages/GPU.cmake
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@ -64,6 +64,8 @@ if(GPU_API STREQUAL "CUDA")
endif()
set(GPU_CUDA_MPS_FLAGS "-DCUDA_MPS_SUPPORT")
endif()
option(CUDA_BUILD_MULTIARCH "Enable building CUDA kernels for all supported GPU architectures" ON)
mark_as_advanced(GPU_BUILD_MULTIARCH)
set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
@ -93,6 +95,7 @@ if(GPU_API STREQUAL "CUDA")
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
if(CUDA_BUILD_MULTIARCH)
# apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
# only the Kepler achitecture and beyond is supported
# comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
@ -145,6 +148,7 @@ if(GPU_API STREQUAL "CUDA")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
endif()
endif()
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} -DLAMMPS_${LAMMPS_SIZES})

4
cmake/Modules/Tools.cmake
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@ -37,7 +37,11 @@ if(BUILD_TOOLS)
add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
endif()
find_package(PkgConfig QUIET)
if(BUILD_LAMMPS_SHELL)
if(NOT PkgConfig_FOUND)
message(FATAL_ERROR "Must have pkg-config installed for building LAMMPS shell")
endif()
find_package(PkgConfig REQUIRED)
pkg_check_modules(READLINE IMPORTED_TARGET REQUIRED readline)
if(NOT LAMMPS_EXCEPTIONS)

14
cmake/presets/macos-multiarch.cmake Normal file
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@ -0,0 +1,14 @@
# preset that will build portable multi-arch binaries on macOS without MPI and OpenMP
set(CMAKE_OSX_ARCHITECTURES "arm64;x86_64" CACHE STRING "" FORCE)
set(CMAKE_OSX_DEPLOYMENT_TARGET 11.0 CACHE STRING "" FORCE)
set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE)
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(BUILD_MPI FALSE CACHE BOOL "" FORCE)
set(BUILD_OMP FALSE CACHE BOOL "" FORCE)
set(BUILD_SHARED_LIBS FALSE CACHE BOOL "" FORCE)

68
doc/src/Build_extras.rst
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@ -140,6 +140,8 @@ CMake build
# value = yes or no (default)
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
# value = yes or no (default)
-D CUDA_BUILD_MULTIARCH=value # enables building CUDA kernels for all supported GPU architectures
# value = yes (default) or no
-D USE_STATIC_OPENCL_LOADER=value # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
# value = yes (default) or no
@ -158,41 +160,49 @@ CMake build
A more detailed list can be found, for example,
at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
CMake can detect which version of the CUDA toolkit is used and thus will try
to include support for **all** major GPU architectures supported by this toolkit.
Thus the GPU_ARCH setting is merely an optimization, to have code for
the preferred GPU architecture directly included rather than having to wait
for the JIT compiler of the CUDA driver to translate it.
CMake can detect which version of the CUDA toolkit is used and thus will
try to include support for **all** major GPU architectures supported by
this toolkit. Thus the GPU_ARCH setting is merely an optimization, to
have code for the preferred GPU architecture directly included rather
than having to wait for the JIT compiler of the CUDA driver to translate
it. This behavior can be turned off (e.g. to speed up compilation) by
setting :code:`CUDA_ENABLE_MULTIARCH` to :code:`no`.
When compiling for CUDA or HIP with CUDA, version 8.0 or later of the CUDA toolkit
is required and a GPU architecture of Kepler or later, which must *also* be
supported by the CUDA toolkit in use **and** the CUDA driver in use.
When compiling for OpenCL, OpenCL version 1.2 or later is required and the
GPU must be supported by the GPU driver and OpenCL runtime bundled with the driver.
When compiling for CUDA or HIP with CUDA, version 8.0 or later of the
CUDA toolkit is required and a GPU architecture of Kepler or later,
which must *also* be supported by the CUDA toolkit in use **and** the
CUDA driver in use. When compiling for OpenCL, OpenCL version 1.2 or
later is required and the GPU must be supported by the GPU driver and
OpenCL runtime bundled with the driver.
When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
using the traditional build procedure. CMake will detect files generated by that
process and will terminate with an error and a suggestion for how to remove them.
When building with CMake, you **must NOT** build the GPU library in
``lib/gpu`` using the traditional build procedure. CMake will detect
files generated by that process and will terminate with an error and a
suggestion for how to remove them.
If you are compiling for OpenCL, the default setting is to download, build, and
link with a static OpenCL ICD loader library and standard OpenCL headers. This
way no local OpenCL development headers or library needs to be present and only
OpenCL compatible drivers need to be installed to use OpenCL. If this is not
desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
If you are compiling for OpenCL, the default setting is to download,
build, and link with a static OpenCL ICD loader library and standard
OpenCL headers. This way no local OpenCL development headers or library
needs to be present and only OpenCL compatible drivers need to be
installed to use OpenCL. If this is not desired, you can set
:code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
The GPU library has some multi-thread support using OpenMP. If LAMMPS is built
with ``-D BUILD_OMP=on`` this will also be enabled.
The GPU library has some multi-thread support using OpenMP. If LAMMPS
is built with ``-D BUILD_OMP=on`` this will also be enabled.
If you are compiling with HIP, note that before running CMake you will have to
set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
and the linker to work correctly.
If you are compiling with HIP, note that before running CMake you will
have to set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are
necessary for :code:`hipcc` and the linker to work correctly.
Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must
set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not
yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you
should only use this option in preparations to run on Aurora system at ANL.
.. versionadded:: 3Aug2022
Using the CHIP-SPV implementation of HIP is supported. It allows one to
run HIP code on Intel GPUs via the OpenCL or Level Zero backends. To use
CHIP-SPV, you must set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake
command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
the use of HIP for Intel GPUs is experimental. You should only use this
option in preparations to run on Aurora system at Argonne.
.. code:: bash

42
doc/src/Modify_style.rst
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@ -28,20 +28,34 @@ Include files (varied)
packages and hard-to-find bugs have regularly manifested in the
past.
- Header files, especially those defining a "style", should only use
the absolute minimum number of include files and **must not**
contain any ``using`` statements. Typically, that would only be the
header for the base class. Instead, any include statements should
be put in the corresponding implementation files and forward
declarations be used. For implementation files, the "include what
you use" principle should be employed. However, there is the
notable exception that when the ``pointers.h`` header is included
(or one of the base classes derived from it) certain headers will
always be included and thus do not need to be explicitly specified.
These are: `mpi.h`, `cstddef`, `cstdio`, `cstdlib`, `string`,
`utils.h`, `vector`, `fmt/format.h`, `climits`, `cinttypes`. This
also means any such file can assume that `FILE`, `NULL`, and
`INT_MAX` are defined.
- Header files, especially those defining a "style", should only use the
absolute minimum number of include files and **must not** contain any
``using`` statements. Typically, that would only be the header for the
base class. Instead, any include statements should be put in the
corresponding implementation files and forward declarations be used.
For implementation files, the "include what you use" principle should
be employed. However, there is the notable exception that when the
``pointers.h`` header is included (or the header of one of the classes
derived from it), certain headers will *always* be included and thus
do not need to be explicitly specified. These are: `mpi.h`,
`cstddef`, `cstdio`, `cstdlib`, `string`, `utils.h`, `vector`,
`fmt/format.h`, `climits`, `cinttypes`. This also means any such file
can assume that `FILE`, `NULL`, and `INT_MAX` are defined.
- Class members variables should not be initialized in the header file,
but instead should be initialized either in the initializer list of
the constructor or explicitly assigned in the body of the constructor.
If the member variable is relevant to the functionality of a class
(for example when it stores a value from a command line argument), the
member variable declaration is followed by a brief comment explaining
its purpose and what its values can be. Class members that are
pointers should always be initialized to ``nullptr`` in the
initializer list of the constructor. This reduces clutter in the
header and avoids accessing uninitialized pointers, which leads to
hard to debug issues, class members are often implicitly initialized
to ``NULL`` on the first use (but *not* after a :doc:`clear command
<clear>`). Please see the files ``reset_atoms_mol.h`` and
``reset_atoms_mol.cpp`` as an example.
- System headers or headers from installed libraries are included with
angular brackets (example: ``#include <vector>``), while local

2
doc/utils/requirements.txt
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@ -1,4 +1,4 @@
Sphinx >= 5.3.0, <7.1.0
Sphinx >= 5.3.0, <7.2.0
sphinxcontrib-spelling
sphinxcontrib-jquery
git+https://github.com/akohlmey/sphinx-fortran@parallel-read

1
doc/utils/sphinx-config/false_positives.txt
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@ -1528,6 +1528,7 @@ inhomogeneous
init
initialdelay
initialisms
initializer
initializations
InitiatorIDs
initio

2
src/.gitignore vendored
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@ -60,6 +60,8 @@
/pair_lepton.h
/pair_lepton_coul.cpp
/pair_lepton_coul.h
/pair_lepton_sphere.cpp
/pair_lepton_sphere.h
/bond_lepton.cpp
/bond_lepton.h
/angle_lepton.cpp

2
src/ELECTRODE/fix_electrode_conp.cpp
View File

@ -417,7 +417,7 @@ void FixElectrodeConp::post_constructor()
input->variable->set(fmt::format("{} equal f_{}[{}]", var_vtop, fixname, 1 + top_group));
input->variable->set(fmt::format("{} equal (v_{}-v_{})/lz", var_efield, var_vbot, var_vtop));
// check for other efields and warn if found
if (modify->get_fix_by_style("efield").size() > 0 && comm->me == 0)
if (modify->get_fix_by_style("^efield").size() > 0 && comm->me == 0)
error->warning(FLERR, "Other efield fixes found -- please make sure this is intended!");
// call fix command:
// fix [varstem]_efield all efield 0.0 0.0 [var_vdiff]/lz

2
src/INTEL/intel_intrinsics_airebo.h
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@ -749,7 +749,7 @@ struct intr_types<float,double> {
#include <cassert>
#include <immintrin.h>
#include <stdint.h> // <cstdint> requires C++-11
#include <cstdint>
#define VEC_INLINE __attribute__((always_inline))

1
src/lmptype.h
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@ -44,7 +44,6 @@
#include <cinttypes> // IWYU pragma: export
#include <climits> // IWYU pragma: export
#include <cstdint> // IWYU pragma: export
#include <cstdlib> // IWYU pragma: export
// grrr - IBM Power6 does not provide this def in their system header files

14
src/thermo.cpp
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@ -1228,13 +1228,13 @@ int Thermo::evaluate_keyword(const std::string &word, double *answer)
} else if (word == "elapsed") {
if (update->whichflag == 0)
error->all(FLERR, "This variable thermo keyword cannot be used between runs");
error->all(FLERR, "This variable thermo keyword elapsed cannot be used between runs");
compute_elapsed();
dvalue = bivalue;
} else if (word == "elaplong") {
if (update->whichflag == 0)
error->all(FLERR, "This variable thermo keyword cannot be used between runs");
error->all(FLERR, "This variable thermo keyword elaplong cannot be used between runs");
compute_elapsed_long();
dvalue = bivalue;
@ -1246,22 +1246,22 @@ int Thermo::evaluate_keyword(const std::string &word, double *answer)
} else if (word == "cpu") {
if (update->whichflag == 0)
error->all(FLERR, "This variable thermo keyword cannot be used between runs");
error->all(FLERR, "This variable thermo keyword cpu cannot be used between runs");
compute_cpu();
} else if (word == "tpcpu") {
if (update->whichflag == 0)
error->all(FLERR, "This variable thermo keyword cannot be used between runs");
error->all(FLERR, "This variable thermo keyword tpcpu cannot be used between runs");
compute_tpcpu();
} else if (word == "spcpu") {
if (update->whichflag == 0)
error->all(FLERR, "This variable thermo keyword cannot be used between runs");
error->all(FLERR, "This variable thermo keyword spcpu cannot be used between runs");
compute_spcpu();
} else if (word == "cpuremain") {
if (update->whichflag == 0)
error->all(FLERR, "This variable thermo keyword cannot be used between runs");
error->all(FLERR, "This variable thermo keyword cpuremain cannot be used between runs");
compute_cpuremain();
} else if (word == "part") {
@ -1350,7 +1350,7 @@ int Thermo::evaluate_keyword(const std::string &word, double *answer)
} else if (word == "etail") {
if (update->eflag_global != update->ntimestep)
error->all(FLERR, "Energy was not tallied on needed timestep");
error->all(FLERR, "Energy was not tallied on needed timestep for thermo keyword etail");
compute_etail();
} else if (word == "enthalpy") {

6
tools/vim/lammps.vim
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@ -17,19 +17,19 @@ syn keyword lammpsLattice delete_atoms displace_atoms change_box dimension
syn keyword lammpsParticle pair_coeff pair_style pair_modify pair_write mass velocity angle_coeff angle_style angle_write
syn keyword lammpsParticle atom_modify atom_style bond_coeff bond_style bond_write create_bonds delete_bonds kspace_style
syn keyword lammpsParticle kspace_modify dihedral_style dihedral_coeff dihedral_write improper_style improper_coeff labelmap
syn keyword lammpsSetup min_style min_modify fix_modify run_style timestep neighbor neigh_modify fix unfix suffix special_bonds
syn keyword lammpsSetup min_style min_modify fix_modify run_style timestep neighbor neigh_modify fix unfix suffix special_bonds dump_modify
syn keyword lammpsSetup balance box clear comm_modify comm_style newton package processors reset_atoms reset_ids reset_timestep
syn keyword lammpsRun minimize minimize/kk run rerun tad neb neb/spin prd quit server temper/npt temper/grem temper
syn keyword lammpsRun message hyper dynamical_matrix dynamical_matrix/kk third_order third_order/kk fitpod
syn keyword lammpsDefine variable group compute python set uncompute kim_query kim group2ndx ndx2group mdi
syn keyword lammpsRepeat jump next loop
syn keyword lammpsRepeat jump next loop label
syn keyword lammpsOperator equal add sub mult div
syn keyword lammpsConditional if then elif else
syn keyword lammpsSpecial EDGE NULL &
syn keyword lammpsSpecial EDGE NULL INF &
syn region lammpsString start=+'+ end=+'+ oneline
syn region lammpsString start=+"+ end=+"+ oneline

3
unittest/force-styles/CMakeLists.txt
View File

@ -199,6 +199,9 @@ add_executable(test_fix_timestep test_fix_timestep.cpp)
if(NOT BUILD_SHARED_LIBS)
target_compile_definitions(test_fix_timestep PRIVATE USING_STATIC_LIBS=1)
endif()
if(FFT_SINGLE)
target_compile_definitions(test_fix_timestep PRIVATE -DFFT_SINGLE)
endif()
target_link_libraries(test_fix_timestep PRIVATE lammps style_tests)
# tests for timestep related fixes (time integration, thermostat, force manipulation, constraints/restraints)

9
unittest/force-styles/test_fix_timestep.cpp
View File

@ -279,6 +279,10 @@ TEST(FixTimestep, plain)
ASSERT_EQ(lmp->atom->natoms, nlocal);
double epsilon = test_config.epsilon;
// relax test precision when using pppm and single precision FFTs
#if defined(FFT_SINGLE)
if (lmp->force->kspace && utils::strmatch(lmp->force->kspace_style, "^pppm")) epsilon *= 2.0e8;
#endif
ErrorStats stats;
@ -411,7 +415,6 @@ TEST(FixTimestep, plain)
ifix = lmp->modify->find_fix("test");
if (!utils::strmatch(lmp->modify->fix[ifix]->style, "^rigid") &&
!utils::strmatch(lmp->modify->fix[ifix]->style, "^nve/limit")) {
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
@ -579,6 +582,10 @@ TEST(FixTimestep, omp)
ASSERT_EQ(lmp->atom->natoms, nlocal);
double epsilon = test_config.epsilon;
// relax test precision when using pppm and single precision FFTs
#if defined(FFT_SINGLE)
if (lmp->force->kspace && utils::strmatch(lmp->force->kspace_style, "^pppm")) epsilon *= 2.0e8;
#endif
ErrorStats stats;